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/8e6k_27921.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8e6k_27921.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8e6k_27921.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8e6k_27921.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8e6k_27921.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8e6k_27921.map" } resolution = 3.1 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= 0.013 sd= 0.074 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 30 5.16 5 C 2969 2.51 5 N 799 2.21 5 O 924 1.98 5 H 4501 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 9223 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 5754 Classifications: {'peptide': 385} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "I" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1641 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Time building chain proxies: 1.48, per 1000 atoms: 0.16 Number of scatterers: 9223 At special positions: 0 Unit cell: (110.2, 121.075, 84.1, 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 30 16.00 O 924 8.00 N 799 7.00 C 2969 6.00 H 4501 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " 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: 2.05 Conformation dependent library (CDL) restraints added in 288.3 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 3.6% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 412B through 413 No H-bonds generated for 'chain 'A' and resid 412B through 413' Processing helix chain 'I' and resid 80 through 82 No H-bonds generated for 'chain 'I' and resid 80 through 82' Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.034A pdb=" N SER A 160 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE A 173 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 179 through 184 removed outlier: 5.864A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 231 through 233 removed outlier: 5.045A pdb=" N TYR A 252 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 264 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU A 258 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 279 through 283 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.911A pdb=" N MET A 376 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP A 396 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TRP A 378 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG A 394 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 407 through 412 removed outlier: 5.407A pdb=" N CYS A 447 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE A 99 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A 449 " --> pdb=" O TRP A 97 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP A 97 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 5 through 7 Processing sheet with id= H, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.846A pdb=" N LYS I 103 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA I 13 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU I 105 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 8 Processing sheet with id= J, first strand: chain 'E' and resid 107 through 109 removed outlier: 5.747A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 387 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: 1.65 Time building geometry restraints manager: 2.33 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: 4500 1.14 - 1.31: 773 1.31 - 1.48: 2087 1.48 - 1.65: 1949 1.65 - 1.82: 39 Bond restraints: 9348 Sorted by residual: bond pdb=" N GLN E 39 " pdb=" H GLN E 39 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N GLY I 64 " pdb=" H GLY I 64 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" N VAL A 411 " pdb=" H VAL A 411 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" N VAL E 98 " pdb=" H VAL E 98 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" N GLY A 248 " pdb=" H GLY A 248 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.60e+01 ... (remaining 9343 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 204 106.97 - 113.73: 10859 113.73 - 120.49: 2840 120.49 - 127.24: 2816 127.24 - 134.00: 79 Bond angle restraints: 16798 Sorted by residual: angle pdb=" N SER A 319 " pdb=" CA SER A 319 " pdb=" C SER A 319 " ideal model delta sigma weight residual 110.35 114.29 -3.94 1.40e+00 5.10e-01 7.92e+00 angle pdb=" C TRP E 35A" pdb=" N GLY E 35B" pdb=" CA GLY E 35B" ideal model delta sigma weight residual 121.05 116.81 4.24 1.85e+00 2.92e-01 5.25e+00 angle pdb=" C CYS A 318 " pdb=" N SER A 319 " pdb=" CA SER A 319 " ideal model delta sigma weight residual 121.31 124.59 -3.28 1.49e+00 4.50e-01 4.84e+00 angle pdb=" N GLY I 66 " pdb=" CA GLY I 66 " pdb=" C GLY I 66 " ideal model delta sigma weight residual 111.63 114.05 -2.42 1.15e+00 7.56e-01 4.42e+00 angle pdb=" C ASN A 104 " pdb=" N GLY A 105 " pdb=" CA GLY A 105 " ideal model delta sigma weight residual 119.94 122.06 -2.12 1.11e+00 8.12e-01 3.63e+00 ... (remaining 16793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 4088 15.41 - 30.83: 257 30.83 - 46.24: 109 46.24 - 61.65: 46 61.65 - 77.07: 7 Dihedral angle restraints: 4507 sinusoidal: 2406 harmonic: 2101 Sorted by residual: dihedral pdb=" CA TYR E 34 " pdb=" C TYR E 34 " pdb=" N TYR E 35 " pdb=" CA TYR E 35 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA VAL A 116 " pdb=" C VAL A 116 " pdb=" N ILE A 117 " pdb=" CA ILE A 117 " ideal model delta harmonic sigma weight residual -180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 64.37 28.63 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 4504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 383 0.029 - 0.058: 222 0.058 - 0.087: 40 0.087 - 0.117: 46 0.117 - 0.146: 18 Chirality restraints: 709 Sorted by residual: chirality pdb=" CA ILE A 192 " pdb=" N ILE A 192 " pdb=" C ILE A 192 " pdb=" CB ILE A 192 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE E 37 " pdb=" N ILE E 37 " pdb=" C ILE E 37 " pdb=" CB ILE E 37 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 706 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 161 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 162 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 66 " 0.093 9.50e-02 1.11e+02 3.12e-02 1.31e+00 pdb=" NE ARG E 66 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG E 66 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 66 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 66 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 66 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 66 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG E 66 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 66 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 412A" -0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 412B" 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 412B" -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 412B" -0.015 5.00e-02 4.00e+02 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.12: 477 2.12 - 2.74: 15109 2.74 - 3.36: 25787 3.36 - 3.98: 36792 3.98 - 4.60: 54052 Nonbonded interactions: 132217 Sorted by model distance: nonbonded pdb=" HG1 THR A 242 " pdb=" O TYR A 275 " model vdw 1.495 1.850 nonbonded pdb=" H TYR A 100 " pdb=" O SER A 445 " model vdw 1.497 1.850 nonbonded pdb=" H ARG E 38 " pdb=" O GLU E 46 " model vdw 1.537 1.850 nonbonded pdb=" O LYS A 150 " pdb=" HG SER A 153 " model vdw 1.543 1.850 nonbonded pdb=" OG SER A 279 " pdb=" HG SER A 409 " model vdw 1.548 1.850 ... (remaining 132212 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=0.51 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: 0.130 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: 0.050 Extract box with map and model: 0.330 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.160 Find NCS groups from input model: 0.060 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:7.070 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.002 0.021 4847 Z= 0.161 Angle : 0.536 4.239 6597 Z= 0.305 Chirality : 0.045 0.146 709 Planarity : 0.004 0.038 852 Dihedral : 11.700 77.068 1719 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 0.57 % Allowed : 4.73 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: -0.56 (0.33), residues: 608 helix: -2.12 (1.05), residues: 7 sheet: 0.02 (0.33), residues: 223 loop : -0.55 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 66 TYR 0.009 0.001 TYR A 316 PHE 0.014 0.002 PHE A 410 TRP 0.010 0.001 TRP E 35A HIS 0.005 0.001 HIS A 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 CYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8117 (m) outliers start: 3 outliers final: 1 residues processed: 109 average time/residue: 0.1473 time to fit residues: 22.1186 Evaluate side-chains 78 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 252 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 GLN I 55 GLN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4847 Z= 0.267 Angle : 0.572 5.511 6597 Z= 0.306 Chirality : 0.047 0.147 709 Planarity : 0.004 0.028 852 Dihedral : 6.286 58.419 667 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.70 % Allowed : 8.71 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: -0.15 (0.34), residues: 608 helix: -1.90 (1.40), residues: 7 sheet: 0.17 (0.32), residues: 236 loop : -0.16 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 327 TYR 0.011 0.002 TYR I 92 PHE 0.014 0.002 PHE A 115 TRP 0.011 0.002 TRP A 456 HIS 0.006 0.002 HIS A 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: A 437 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7896 (mt) REVERT: E 25 SER cc_start: 0.7545 (t) cc_final: 0.7292 (p) outliers start: 9 outliers final: 4 residues processed: 83 average time/residue: 0.1986 time to fit residues: 23.2113 Evaluate side-chains 77 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain E residue 18 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN I 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4847 Z= 0.264 Angle : 0.540 5.459 6597 Z= 0.292 Chirality : 0.046 0.154 709 Planarity : 0.004 0.027 852 Dihedral : 6.049 54.302 667 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 1.52 % Allowed : 10.98 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: -0.15 (0.34), residues: 608 helix: -1.83 (1.49), residues: 7 sheet: 0.15 (0.32), residues: 242 loop : -0.15 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.010 0.002 TYR A 406 PHE 0.015 0.002 PHE A 115 TRP 0.011 0.001 TRP A 178 HIS 0.006 0.002 HIS A 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: E 25 SER cc_start: 0.7769 (t) cc_final: 0.7469 (p) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.1381 time to fit residues: 14.7159 Evaluate side-chains 80 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain E residue 18 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 0.3980 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4847 Z= 0.230 Angle : 0.517 4.459 6597 Z= 0.280 Chirality : 0.046 0.149 709 Planarity : 0.003 0.030 852 Dihedral : 5.811 48.219 667 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.89 % Rotamer: Outliers : 1.70 % Allowed : 10.23 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % 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: -0.05 (0.35), residues: 608 helix: -1.36 (1.59), residues: 7 sheet: 0.23 (0.32), residues: 241 loop : -0.10 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.010 0.001 TYR E 58 PHE 0.013 0.002 PHE A 115 TRP 0.012 0.001 TRP A 178 HIS 0.004 0.001 HIS A 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: E 25 SER cc_start: 0.7830 (t) cc_final: 0.7524 (p) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.1152 time to fit residues: 13.5510 Evaluate side-chains 77 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain E residue 18 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4847 Z= 0.360 Angle : 0.583 5.518 6597 Z= 0.317 Chirality : 0.047 0.151 709 Planarity : 0.004 0.032 852 Dihedral : 6.057 45.650 667 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 2.08 % Allowed : 11.17 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.40 (0.35), residues: 608 helix: -1.27 (1.78), residues: 7 sheet: -0.04 (0.32), residues: 247 loop : -0.34 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 327 TYR 0.013 0.002 TYR I 92 PHE 0.016 0.002 PHE A 115 TRP 0.011 0.002 TRP A 361 HIS 0.007 0.002 HIS A 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: A 275 TYR cc_start: 0.8603 (m-80) cc_final: 0.8384 (m-80) REVERT: E 7 SER cc_start: 0.8134 (t) cc_final: 0.7786 (m) REVERT: E 25 SER cc_start: 0.7916 (t) cc_final: 0.7589 (p) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.1305 time to fit residues: 14.5554 Evaluate side-chains 80 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain E residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4847 Z= 0.188 Angle : 0.517 5.008 6597 Z= 0.276 Chirality : 0.046 0.151 709 Planarity : 0.004 0.032 852 Dihedral : 5.679 45.176 667 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.28 % Favored : 95.56 % Rotamer: Outliers : 0.95 % Allowed : 13.45 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.25 (0.35), residues: 608 helix: -1.33 (1.60), residues: 7 sheet: 0.09 (0.33), residues: 241 loop : -0.25 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.009 0.001 TYR I 36 PHE 0.011 0.001 PHE E 78 TRP 0.017 0.001 TRP A 178 HIS 0.003 0.001 HIS A 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 748.24 seconds wall clock time: 13 minutes 21.56 seconds (801.56 seconds total)