Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8dl8_27499.map" } resolution = 3.0 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.069 sd= 0.195 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 4311 2.51 5 N 1096 2.21 5 O 1269 1.98 5 H 6701 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 190": "OD1" <-> "OD2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 13419 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6914 Inner-chain residues flagged as termini: ['pdbres="GLY A 238 "', 'pdbres="CYS A 284 "', 'pdbres="PRO A 397 "', 'pdbres="PRO A 451 "'] Classifications: {'peptide': 445} Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2} Link IDs: {'PTRANS': 11, 'TRANS': 433} Chain breaks: 2 Chain: "C" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3220 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "D" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3285 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 204} Time building chain proxies: 2.20, per 1000 atoms: 0.16 Number of scatterers: 13419 At special positions: 0 Unit cell: (73.44, 76.68, 147.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 1269 8.00 N 1096 7.00 C 4311 6.00 H 6701 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 485.4 milliseconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 45.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 24 through 53 Processing helix chain 'A' and resid 58 through 84 removed outlier: 5.330A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 127 through 155 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.693A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 285 through 304 removed outlier: 4.662A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.639A pdb=" N TYR A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 369 through 391 Processing helix chain 'A' and resid 452 through 482 Processing helix chain 'A' and resid 489 through 513 Processing helix chain 'A' and resid 517 through 546 removed outlier: 4.412A pdb=" N GLY A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing sheet with id= A, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.546A pdb=" N LYS C 123 " --> pdb=" O MET C 31 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR C 33 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU C 125 " --> pdb=" O THR C 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.698A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 105 through 110 removed outlier: 3.590A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 135 through 138 removed outlier: 3.567A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 165 through 170 Processing sheet with id= F, first strand: chain 'D' and resid 22 through 25 Processing sheet with id= G, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.583A pdb=" N GLY D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LYS D 57 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP D 66 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ARG D 59 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 64 " --> pdb=" O ARG D 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 145 through 149 removed outlier: 3.636A pdb=" N LEU D 166 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR D 200 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 175 through 179 removed outlier: 4.928A pdb=" N ILE D 218 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 194 through 196 403 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 6692 1.14 - 1.31: 1079 1.31 - 1.48: 2839 1.48 - 1.65: 2896 1.65 - 1.82: 65 Bond restraints: 13571 Sorted by residual: bond pdb=" N ALA C 150 " pdb=" H ALA C 150 " ideal model delta sigma weight residual 0.860 1.034 -0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" N THR D 209 " pdb=" H THR D 209 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N GLY C 149 " pdb=" H GLY C 149 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N SER C 72 " pdb=" H SER C 72 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N VAL D 161 " pdb=" H VAL D 161 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 13566 not shown) Histogram of bond angle deviations from ideal: 95.82 - 103.54: 76 103.54 - 111.25: 15074 111.25 - 118.97: 3530 118.97 - 126.68: 5708 126.68 - 134.40: 120 Bond angle restraints: 24508 Sorted by residual: angle pdb=" N GLY D 169 " pdb=" CA GLY D 169 " pdb=" C GLY D 169 " ideal model delta sigma weight residual 113.76 105.99 7.77 1.80e+00 3.09e-01 1.86e+01 angle pdb=" N THR D 209 " pdb=" CA THR D 209 " pdb=" C THR D 209 " ideal model delta sigma weight residual 111.07 114.52 -3.45 1.07e+00 8.73e-01 1.04e+01 angle pdb=" CB THR D 142 " pdb=" CG2 THR D 142 " pdb="HG22 THR D 142 " ideal model delta sigma weight residual 110.00 101.72 8.28 3.00e+00 1.11e-01 7.61e+00 angle pdb=" N PRO D 172 " pdb=" CA PRO D 172 " pdb=" C PRO D 172 " ideal model delta sigma weight residual 112.47 117.64 -5.17 2.06e+00 2.36e-01 6.29e+00 angle pdb=" CA TYR D 170 " pdb=" CB TYR D 170 " pdb=" CG TYR D 170 " ideal model delta sigma weight residual 113.90 118.38 -4.48 1.80e+00 3.09e-01 6.18e+00 ... (remaining 24503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5693 17.39 - 34.78: 489 34.78 - 52.17: 196 52.17 - 69.56: 59 69.56 - 86.95: 5 Dihedral angle restraints: 6442 sinusoidal: 3443 harmonic: 2999 Sorted by residual: dihedral pdb=" CA GLY D 169 " pdb=" C GLY D 169 " pdb=" N TYR D 170 " pdb=" CA TYR D 170 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER C 194 " pdb=" C SER C 194 " pdb=" N MET C 195 " pdb=" CA MET C 195 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER C 228 " pdb=" C SER C 228 " pdb=" N PHE C 229 " pdb=" CA PHE C 229 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 756 0.036 - 0.071: 236 0.071 - 0.107: 69 0.107 - 0.143: 26 0.143 - 0.179: 3 Chirality restraints: 1090 Sorted by residual: chirality pdb=" CA ILE C 164 " pdb=" N ILE C 164 " pdb=" C ILE C 164 " pdb=" CB ILE C 164 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA PRO D 172 " pdb=" N PRO D 172 " pdb=" C PRO D 172 " pdb=" CB PRO D 172 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE D 235 " pdb=" CA ILE D 235 " pdb=" CG1 ILE D 235 " pdb=" CG2 ILE D 235 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1087 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 143 " -0.042 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO D 144 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 516 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 517 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 213 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 214 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " -0.029 5.00e-02 4.00e+02 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 230 1.95 - 2.61: 14140 2.61 - 3.28: 40360 3.28 - 3.94: 52198 3.94 - 4.60: 77635 Nonbonded interactions: 184563 Sorted by model distance: nonbonded pdb=" O SER C 141 " pdb=" H LEU C 145 " model vdw 1.288 1.850 nonbonded pdb=" HG1 THR C 184 " pdb=" O SER C 194 " model vdw 1.375 1.850 nonbonded pdb=" OG SER C 141 " pdb=" H GLN C 144 " model vdw 1.457 1.850 nonbonded pdb=" O GLY A 368 " pdb=" HG1 THR A 372 " model vdw 1.520 1.850 nonbonded pdb=" O ILE A 354 " pdb=" HG1 THR A 357 " model vdw 1.556 1.850 ... (remaining 184558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.47 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.350 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.760 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:10.450 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6870 Z= 0.214 Angle : 0.586 7.768 9354 Z= 0.316 Chirality : 0.041 0.179 1090 Planarity : 0.006 0.065 1166 Dihedral : 14.872 86.950 2413 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 2.15 % Allowed : 19.92 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.29), residues: 867 helix: 1.66 (0.25), residues: 394 sheet: 0.46 (0.38), residues: 207 loop : -1.38 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 74 TYR 0.014 0.001 TYR D 170 PHE 0.019 0.002 PHE D 191 TRP 0.015 0.001 TRP D 213 HIS 0.007 0.001 HIS D 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 263 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ASN cc_start: 0.8638 (t0) cc_final: 0.8389 (t0) REVERT: D 62 GLN cc_start: 0.8459 (tp40) cc_final: 0.7685 (mp10) outliers start: 16 outliers final: 7 residues processed: 271 average time/residue: 1.4177 time to fit residues: 410.0390 Evaluate side-chains 180 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 173 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain C residue 34 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 232 ASN D 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6870 Z= 0.284 Angle : 0.600 6.416 9354 Z= 0.319 Chirality : 0.040 0.152 1090 Planarity : 0.006 0.064 1166 Dihedral : 5.645 66.710 951 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 3.36 % Allowed : 28.53 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 867 helix: 2.38 (0.26), residues: 394 sheet: 0.86 (0.38), residues: 201 loop : -1.27 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 208 TYR 0.013 0.001 TYR D 170 PHE 0.017 0.001 PHE C 229 TRP 0.011 0.001 TRP D 213 HIS 0.013 0.002 HIS C 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8199 (t70) cc_final: 0.7976 (t70) REVERT: C 48 ASN cc_start: 0.8691 (t0) cc_final: 0.8433 (t0) outliers start: 25 outliers final: 13 residues processed: 196 average time/residue: 0.8438 time to fit residues: 177.6502 Evaluate side-chains 172 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 221 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 40.0000 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 144 GLN C 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6870 Z= 0.228 Angle : 0.588 6.192 9354 Z= 0.312 Chirality : 0.039 0.142 1090 Planarity : 0.005 0.061 1166 Dihedral : 5.225 61.648 945 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 3.63 % Allowed : 30.15 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.30), residues: 867 helix: 2.60 (0.26), residues: 394 sheet: 1.02 (0.39), residues: 199 loop : -1.12 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 175 TYR 0.014 0.001 TYR C 206 PHE 0.018 0.001 PHE C 229 TRP 0.007 0.001 TRP D 179 HIS 0.014 0.002 HIS C 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8174 (t80) REVERT: C 48 ASN cc_start: 0.8666 (t0) cc_final: 0.8427 (t0) REVERT: D 59 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7941 (ttp-110) REVERT: D 62 GLN cc_start: 0.8471 (tp40) cc_final: 0.8241 (tp40) outliers start: 27 outliers final: 16 residues processed: 180 average time/residue: 0.7609 time to fit residues: 147.4135 Evaluate side-chains 168 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 221 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 chunk 26 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6870 Z= 0.259 Angle : 0.606 7.920 9354 Z= 0.316 Chirality : 0.040 0.140 1090 Planarity : 0.005 0.059 1166 Dihedral : 5.078 59.875 945 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 3.50 % Allowed : 31.49 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.30), residues: 867 helix: 2.72 (0.26), residues: 390 sheet: 1.11 (0.39), residues: 199 loop : -1.09 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.011 0.001 TYR D 170 PHE 0.014 0.001 PHE C 155 TRP 0.009 0.001 TRP C 183 HIS 0.009 0.001 HIS A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 160 average time/residue: 0.7484 time to fit residues: 128.8793 Evaluate side-chains 154 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 221 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 overall best weight: 7.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 186 GLN C 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6870 Z= 0.288 Angle : 0.608 6.208 9354 Z= 0.323 Chirality : 0.040 0.157 1090 Planarity : 0.006 0.078 1166 Dihedral : 4.950 59.433 945 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 3.63 % Allowed : 31.63 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.29), residues: 867 helix: 2.59 (0.26), residues: 392 sheet: 1.05 (0.39), residues: 199 loop : -1.03 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 32 TYR 0.012 0.001 TYR C 69 PHE 0.018 0.001 PHE C 155 TRP 0.008 0.001 TRP C 183 HIS 0.010 0.002 HIS A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 227 is missing expected H atoms. Skipping. Residue THR 142 is missing expected H atoms. Skipping. Residue TYR 170 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.8012 (ttp-110) REVERT: D 61 GLU cc_start: 0.7832 (pp20) cc_final: 0.7158 (pp20) REVERT: D 62 GLN cc_start: 0.8363 (tp40) cc_final: 0.8000 (mm110) outliers start: 27 outliers final: 17 residues processed: 155 average time/residue: 0.7261 time to fit residues: 120.7252 Evaluate side-chains 152 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 221 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 40.0000 chunk 63 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 118 HIS A 493 ASN C 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6870 Z= 0.207 Angle : 0.625 10.511 9354 Z= 0.318 Chirality : 0.040 0.139 1090 Planarity : 0.005 0.070 1166 Dihedral : 4.413 34.791 943 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.42 % Allowed : 33.38 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.29), residues: 867 helix: 2.63 (0.26), residues: 393 sheet: 0.95 (0.39), residues: 201 loop : -0.92 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 32 TYR 0.015 0.001 TYR D 170 PHE 0.021 0.001 PHE C 155 TRP 0.008 0.001 TRP D 69 HIS 0.011 0.002 HIS D 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.34 seconds wall clock time: 24 minutes 49.01 seconds (1489.01 seconds total)