Starting phenix.real_space_refine on Sun May 19 16:30:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.19 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vxz_32189.map" } resolution = 3.19 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= 0.005 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 856 atoms to isotropic. 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 45 5.16 5 C 4610 2.51 5 N 1223 2.21 5 O 1399 1.98 5 H 7071 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 213": "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: 14348 Number of models: 1 Model: "" Number of chains: 5 Chain: "0" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3851 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 238} Chain: "1" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3592 Classifications: {'peptide': 237} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "2" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 864 Inner-chain residues flagged as termini: ['pdbres="HIS 2 13 "', 'pdbres="ILE 2 25 "'] Classifications: {'peptide': 56} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain breaks: 1 Chain: "3" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1849 Classifications: {'peptide': 118} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "4" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4192 Classifications: {'peptide': 268} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 248} Time building chain proxies: 2.33, per 1000 atoms: 0.16 Number of scatterers: 14348 At special positions: 0 Unit cell: (128.52, 97.2, 92.88, 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 45 16.00 O 1399 8.00 N 1223 7.00 C 4610 6.00 H 7071 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 101 " distance=2.04 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: 3.12 Conformation dependent library (CDL) restraints added in 442.5 milliseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 8.5% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain '0' and resid 82 through 88 removed outlier: 3.689A pdb=" N LEU 0 86 " --> pdb=" O LEU 0 82 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER 0 87 " --> pdb=" O PRO 0 83 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN 0 88 " --> pdb=" O ASP 0 84 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 82 through 88' Processing helix chain '0' and resid 90 through 98 Processing helix chain '0' and resid 143 through 146 No H-bonds generated for 'chain '0' and resid 143 through 146' Processing helix chain '0' and resid 181 through 186 removed outlier: 4.107A pdb=" N THR 0 185 " --> pdb=" O GLY 0 182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE 0 186 " --> pdb=" O ASN 0 183 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 48 Processing helix chain '1' and resid 61 through 63 No H-bonds generated for 'chain '1' and resid 61 through 63' Processing helix chain '1' and resid 99 through 106 removed outlier: 4.375A pdb=" N TYR 1 106 " --> pdb=" O GLU 1 102 " (cutoff:3.500A) Processing helix chain '1' and resid 145 through 150 removed outlier: 3.995A pdb=" N LEU 1 150 " --> pdb=" O VAL 1 146 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 54 removed outlier: 3.765A pdb=" N THR 2 54 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Processing helix chain '4' and resid 44 through 47 No H-bonds generated for 'chain '4' and resid 44 through 47' Processing helix chain '4' and resid 64 through 68 Processing helix chain '4' and resid 94 through 96 No H-bonds generated for 'chain '4' and resid 94 through 96' Processing helix chain '4' and resid 98 through 106 Processing helix chain '4' and resid 157 through 160 Processing sheet with id= A, first strand: chain '0' and resid 14 through 18 Processing sheet with id= B, first strand: chain '0' and resid 63 through 65 Processing sheet with id= C, first strand: chain '0' and resid 78 through 81 Processing sheet with id= D, first strand: chain '0' and resid 101 through 103 Processing sheet with id= E, first strand: chain '1' and resid 70 through 73 Processing sheet with id= F, first strand: chain '1' and resid 109 through 111 removed outlier: 3.501A pdb=" N HIS 1 109 " --> pdb=" O ARG 1 223 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 152 through 157 removed outlier: 3.833A pdb=" N LYS 1 129 " --> pdb=" O THR 1 196 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU 1 131 " --> pdb=" O TYR 1 194 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR 1 194 " --> pdb=" O LEU 1 131 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA 1 133 " --> pdb=" O CYS 1 192 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N CYS 1 192 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER 1 135 " --> pdb=" O ILE 1 190 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE 1 190 " --> pdb=" O SER 1 135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE 1 83 " --> pdb=" O CYS 1 192 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR 1 194 " --> pdb=" O GLN 1 81 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN 1 81 " --> pdb=" O TYR 1 194 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '2' and resid 4 through 7 Processing sheet with id= I, first strand: chain '3' and resid 7 through 12 removed outlier: 8.800A pdb=" N GLU 3 8 " --> pdb=" O ASN 3 111 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS 3 113 " --> pdb=" O GLU 3 8 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE 3 10 " --> pdb=" O LYS 3 113 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS 3 115 " --> pdb=" O ILE 3 10 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LYS 3 12 " --> pdb=" O HIS 3 115 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL 3 117 " --> pdb=" O LYS 3 12 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE 3 40 " --> pdb=" O VAL 3 51 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL 3 51 " --> pdb=" O ILE 3 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 18 through 20 removed outlier: 3.629A pdb=" N HIS 3 73 " --> pdb=" O ASN 3 87 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '4' and resid 87 through 91 Processing sheet with id= L, first strand: chain '4' and resid 109 through 111 removed outlier: 3.523A pdb=" N TYR 4 109 " --> pdb=" O TRP 4 245 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 177 through 180 removed outlier: 3.929A pdb=" N TYR 4 75 " --> pdb=" O ILE 4 235 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE 4 237 " --> pdb=" O CYS 4 73 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N CYS 4 73 " --> pdb=" O PHE 4 237 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 414 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: 2.33 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 7052 1.15 - 1.31: 1218 1.31 - 1.48: 3095 1.48 - 1.65: 3102 1.65 - 1.81: 69 Bond restraints: 14536 Sorted by residual: bond pdb=" N TRP 4 159 " pdb=" H TRP 4 159 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N SER 3 85 " pdb=" H SER 3 85 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N ILE 4 207 " pdb=" H ILE 4 207 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" N HIS 0 118 " pdb=" H HIS 0 118 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N ASN 0 165 " pdb=" H ASN 0 165 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 14531 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 370 106.98 - 113.74: 17170 113.74 - 120.50: 4438 120.50 - 127.26: 4122 127.26 - 134.02: 106 Bond angle restraints: 26206 Sorted by residual: angle pdb=" CA TRP 4 159 " pdb=" C TRP 4 159 " pdb=" N GLN 4 160 " ideal model delta sigma weight residual 116.84 121.27 -4.43 1.71e+00 3.42e-01 6.73e+00 angle pdb=" N GLY 0 90 " pdb=" CA GLY 0 90 " pdb=" C GLY 0 90 " ideal model delta sigma weight residual 112.45 117.81 -5.36 2.10e+00 2.27e-01 6.52e+00 angle pdb=" C ILE 3 52 " pdb=" N ILE 3 53 " pdb=" CA ILE 3 53 " ideal model delta sigma weight residual 122.71 119.20 3.51 1.44e+00 4.82e-01 5.95e+00 angle pdb=" N THR 4 276 " pdb=" CA THR 4 276 " pdb=" C THR 4 276 " ideal model delta sigma weight residual 113.56 110.47 3.09 1.39e+00 5.18e-01 4.94e+00 angle pdb=" C LEU 1 132 " pdb=" N ALA 1 133 " pdb=" CA ALA 1 133 " ideal model delta sigma weight residual 121.85 118.10 3.75 1.77e+00 3.19e-01 4.50e+00 ... (remaining 26201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 6339 15.22 - 30.44: 413 30.44 - 45.67: 148 45.67 - 60.89: 79 60.89 - 76.11: 3 Dihedral angle restraints: 6982 sinusoidal: 3753 harmonic: 3229 Sorted by residual: dihedral pdb=" CA TYR 0 106 " pdb=" C TYR 0 106 " pdb=" N THR 0 107 " pdb=" CA THR 0 107 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" N ASN 4 55 " pdb=" CA ASN 4 55 " pdb=" CB ASN 4 55 " pdb=" CG ASN 4 55 " ideal model delta sinusoidal sigma weight residual -180.00 -120.58 -59.42 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA MET 1 211 " pdb=" CB MET 1 211 " pdb=" CG MET 1 211 " pdb=" SD MET 1 211 " ideal model delta sinusoidal sigma weight residual -60.00 -118.28 58.28 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 722 0.034 - 0.067: 282 0.067 - 0.101: 65 0.101 - 0.134: 55 0.134 - 0.168: 7 Chirality restraints: 1131 Sorted by residual: chirality pdb=" CA VAL 0 124 " pdb=" N VAL 0 124 " pdb=" C VAL 0 124 " pdb=" CB VAL 0 124 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ILE 0 243 " pdb=" N ILE 0 243 " pdb=" C ILE 0 243 " pdb=" CB ILE 0 243 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ILE 1 190 " pdb=" N ILE 1 190 " pdb=" C ILE 1 190 " pdb=" CB ILE 1 190 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1128 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 0 127 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO 0 128 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO 0 128 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO 0 128 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU 2 55 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO 2 56 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO 2 56 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO 2 56 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 0 75 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO 0 76 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO 0 76 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 0 76 " 0.021 5.00e-02 4.00e+02 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 852 2.17 - 2.78: 25150 2.78 - 3.38: 36007 3.38 - 3.99: 49402 3.99 - 4.60: 71603 Nonbonded interactions: 183014 Sorted by model distance: nonbonded pdb=" O THR 1 98 " pdb=" H GLU 1 102 " model vdw 1.560 1.850 nonbonded pdb=" O GLU 0 27 " pdb="HD22 ASN 0 198 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP 0 44 " pdb="HH21 ARG 4 51 " model vdw 1.616 1.850 nonbonded pdb=" HG1 THR 3 17 " pdb=" O THR 3 89 " model vdw 1.618 1.850 nonbonded pdb=" HG1 THR 0 136 " pdb=" O ASN 0 165 " model vdw 1.646 1.850 ... (remaining 183009 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 0.380 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.070 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:10.590 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 0.031 7465 Z= 0.159 Angle : 0.507 5.361 10184 Z= 0.277 Chirality : 0.044 0.168 1131 Planarity : 0.004 0.038 1323 Dihedral : 10.882 75.509 2691 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.10 % Favored : 94.47 % Rotamer: Outliers : 2.47 % Allowed : 5.07 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.69 (0.24), residues: 922 helix: -2.98 (0.45), residues: 67 sheet: 0.18 (0.30), residues: 270 loop : -1.60 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 4 102 TYR 0.015 0.001 TYR 0 173 PHE 0.008 0.001 PHE 1 120 TRP 0.010 0.001 TRP 0 79 HIS 0.003 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 0.365 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: 0 43 LYS cc_start: 0.8149 (mttt) cc_final: 0.7873 (mmtt) REVERT: 0 75 SER cc_start: 0.9091 (m) cc_final: 0.8839 (p) REVERT: 0 106 TYR cc_start: 0.8465 (m-80) cc_final: 0.7326 (m-80) REVERT: 0 108 VAL cc_start: 0.9168 (m) cc_final: 0.8967 (t) REVERT: 0 262 HIS cc_start: 0.7540 (p-80) cc_final: 0.7262 (p-80) REVERT: 1 39 GLU cc_start: 0.7662 (tt0) cc_final: 0.7334 (mm-30) REVERT: 1 53 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8707 (p) REVERT: 1 144 LYS cc_start: 0.9000 (pttm) cc_final: 0.8709 (mtmt) REVERT: 3 59 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7747 (tttt) outliers start: 20 outliers final: 7 residues processed: 242 average time/residue: 0.3381 time to fit residues: 107.3337 Evaluate side-chains 175 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 84 ASP Chi-restraints excluded: chain 0 residue 198 ASN Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 3 residue 40 ILE Chi-restraints excluded: chain 3 residue 52 ILE Chi-restraints excluded: chain 4 residue 55 ASN Chi-restraints excluded: chain 4 residue 253 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 219 ASN 0 262 HIS 3 50 GLN 4 66 ASN 4 132 GLN 4 208 ASN 4 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7465 Z= 0.241 Angle : 0.513 4.951 10184 Z= 0.263 Chirality : 0.044 0.155 1131 Planarity : 0.004 0.038 1323 Dihedral : 5.840 67.177 1024 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 2.35 % Allowed : 9.15 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.32 (0.25), residues: 922 helix: -2.46 (0.46), residues: 69 sheet: 0.36 (0.30), residues: 270 loop : -1.34 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 1 177 TYR 0.012 0.001 TYR 0 173 PHE 0.009 0.001 PHE 2 46 TRP 0.008 0.001 TRP 0 80 HIS 0.003 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: 0 43 LYS cc_start: 0.8253 (mttt) cc_final: 0.7907 (mmtt) REVERT: 0 75 SER cc_start: 0.9180 (m) cc_final: 0.8827 (p) REVERT: 1 39 GLU cc_start: 0.7974 (tt0) cc_final: 0.7323 (mm-30) REVERT: 1 53 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8822 (p) REVERT: 3 59 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7768 (tttt) REVERT: 3 109 VAL cc_start: 0.8634 (t) cc_final: 0.8366 (m) REVERT: 4 28 ILE cc_start: 0.8563 (pt) cc_final: 0.8351 (pt) REVERT: 4 163 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7756 (m) REVERT: 4 264 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8419 (tt0) outliers start: 19 outliers final: 13 residues processed: 183 average time/residue: 0.2461 time to fit residues: 62.1807 Evaluate side-chains 177 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 84 ASP Chi-restraints excluded: chain 0 residue 198 ASN Chi-restraints excluded: chain 0 residue 239 THR Chi-restraints excluded: chain 1 residue 18 ASP Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 58 VAL Chi-restraints excluded: chain 1 residue 135 SER Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 3 residue 52 ILE Chi-restraints excluded: chain 3 residue 79 LEU Chi-restraints excluded: chain 4 residue 40 SER Chi-restraints excluded: chain 4 residue 55 ASN Chi-restraints excluded: chain 4 residue 116 LEU Chi-restraints excluded: chain 4 residue 163 THR Chi-restraints excluded: chain 4 residue 253 CYS Chi-restraints excluded: chain 4 residue 264 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 189 HIS 1 56 GLN 3 50 GLN 4 160 GLN 4 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7465 Z= 0.182 Angle : 0.477 4.729 10184 Z= 0.244 Chirality : 0.043 0.149 1131 Planarity : 0.004 0.038 1323 Dihedral : 5.490 55.209 1022 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 1.98 % Allowed : 10.75 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.13 (0.25), residues: 922 helix: -2.12 (0.49), residues: 69 sheet: 0.35 (0.31), residues: 262 loop : -1.13 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 1 35 TYR 0.012 0.001 TYR 0 173 PHE 0.007 0.001 PHE 4 76 TRP 0.006 0.001 TRP 0 79 HIS 0.004 0.001 HIS 0 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 43 LYS cc_start: 0.8279 (mttt) cc_final: 0.8030 (mmtt) REVERT: 0 75 SER cc_start: 0.9201 (m) cc_final: 0.8796 (p) REVERT: 1 39 GLU cc_start: 0.8012 (tt0) cc_final: 0.7292 (mm-30) REVERT: 1 53 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8825 (p) REVERT: 3 109 VAL cc_start: 0.8652 (t) cc_final: 0.8406 (m) REVERT: 4 13 ARG cc_start: 0.6928 (ttm170) cc_final: 0.6572 (mtt180) REVERT: 4 163 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7881 (m) REVERT: 4 264 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8439 (tt0) outliers start: 16 outliers final: 9 residues processed: 170 average time/residue: 0.2005 time to fit residues: 46.8820 Evaluate side-chains 164 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 84 ASP Chi-restraints excluded: chain 0 residue 198 ASN Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 75 ASN Chi-restraints excluded: chain 1 residue 135 SER Chi-restraints excluded: chain 3 residue 52 ILE Chi-restraints excluded: chain 4 residue 40 SER Chi-restraints excluded: chain 4 residue 55 ASN Chi-restraints excluded: chain 4 residue 116 LEU Chi-restraints excluded: chain 4 residue 163 THR Chi-restraints excluded: chain 4 residue 253 CYS Chi-restraints excluded: chain 4 residue 264 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 69 GLN 3 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7465 Z= 0.299 Angle : 0.521 4.942 10184 Z= 0.267 Chirality : 0.045 0.149 1131 Planarity : 0.004 0.038 1323 Dihedral : 5.561 59.859 1021 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 2.10 % Allowed : 11.37 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.20 (0.25), residues: 922 helix: -1.86 (0.53), residues: 69 sheet: 0.25 (0.30), residues: 267 loop : -1.21 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 4 272 TYR 0.012 0.001 TYR 4 193 PHE 0.015 0.002 PHE 1 95 TRP 0.008 0.001 TRP 1 156 HIS 0.006 0.001 HIS 0 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 43 LYS cc_start: 0.8323 (mttt) cc_final: 0.8048 (mmtt) REVERT: 0 197 ASN cc_start: 0.8181 (t0) cc_final: 0.7946 (t0) REVERT: 1 39 GLU cc_start: 0.8173 (tt0) cc_final: 0.7450 (mm-30) REVERT: 1 53 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8864 (p) REVERT: 1 125 MET cc_start: 0.8929 (mmt) cc_final: 0.8523 (mmt) REVERT: 3 109 VAL cc_start: 0.8730 (t) cc_final: 0.8519 (m) REVERT: 4 55 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8423 (t0) REVERT: 4 163 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7964 (m) REVERT: 4 264 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8490 (tt0) outliers start: 17 outliers final: 11 residues processed: 168 average time/residue: 0.1746 time to fit residues: 40.4436 Evaluate side-chains 165 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 84 ASP Chi-restraints excluded: chain 0 residue 91 LEU Chi-restraints excluded: chain 0 residue 198 ASN Chi-restraints excluded: chain 0 residue 239 THR Chi-restraints excluded: chain 0 residue 262 HIS Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 75 ASN Chi-restraints excluded: chain 1 residue 135 SER Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 4 residue 40 SER Chi-restraints excluded: chain 4 residue 55 ASN Chi-restraints excluded: chain 4 residue 116 LEU Chi-restraints excluded: chain 4 residue 163 THR Chi-restraints excluded: chain 4 residue 253 CYS Chi-restraints excluded: chain 4 residue 264 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7465 Z= 0.194 Angle : 0.478 4.830 10184 Z= 0.242 Chirality : 0.044 0.144 1131 Planarity : 0.004 0.039 1323 Dihedral : 5.256 54.154 1019 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer: Outliers : 1.61 % Allowed : 11.99 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.14 (0.25), residues: 922 helix: -1.61 (0.56), residues: 69 sheet: 0.28 (0.30), residues: 269 loop : -1.20 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 4 272 TYR 0.011 0.001 TYR 0 173 PHE 0.009 0.001 PHE 1 95 TRP 0.007 0.001 TRP 0 80 HIS 0.003 0.001 HIS 4 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 43 LYS cc_start: 0.8308 (mttt) cc_final: 0.8023 (mmtt) REVERT: 0 197 ASN cc_start: 0.8059 (t0) cc_final: 0.7821 (t0) REVERT: 1 39 GLU cc_start: 0.8159 (tt0) cc_final: 0.7472 (mm-30) REVERT: 1 53 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8832 (p) REVERT: 1 125 MET cc_start: 0.8937 (mmt) cc_final: 0.8546 (mmt) REVERT: 1 219 ASP cc_start: 0.8752 (p0) cc_final: 0.8466 (p0) REVERT: 3 109 VAL cc_start: 0.8749 (t) cc_final: 0.8538 (m) REVERT: 4 13 ARG cc_start: 0.7022 (ttm170) cc_final: 0.6711 (mtt180) REVERT: 4 55 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8253 (t0) REVERT: 4 163 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8006 (m) REVERT: 4 264 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8522 (tt0) outliers start: 13 outliers final: 9 residues processed: 168 average time/residue: 0.1754 time to fit residues: 39.8287 Evaluate side-chains 163 residues out of total 809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 84 ASP Chi-restraints excluded: chain 0 residue 198 ASN Chi-restraints excluded: chain 0 residue 239 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 75 ASN Chi-restraints excluded: chain 1 residue 135 SER Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 4 residue 40 SER Chi-restraints excluded: chain 4 residue 55 ASN Chi-restraints excluded: chain 4 residue 116 LEU Chi-restraints excluded: chain 4 residue 163 THR Chi-restraints excluded: chain 4 residue 253 CYS Chi-restraints excluded: chain 4 residue 264 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.0050 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 overall best weight: 2.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7465 Z= 0.127 Angle : 0.445 4.624 10184 Z= 0.222 Chirality : 0.043 0.141 1131 Planarity : 0.003 0.035 1323 Dihedral : 4.850 47.929 1019 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.24 % Allowed : 12.48 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.96 (0.26), residues: 922 helix: -1.41 (0.58), residues: 69 sheet: 0.34 (0.30), residues: 271 loop : -1.04 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 4 95 TYR 0.009 0.001 TYR 0 173 PHE 0.007 0.001 PHE 0 92 TRP 0.009 0.001 TRP 3 38 HIS 0.002 0.001 HIS 4 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 877.45 seconds wall clock time: 15 minutes 34.73 seconds (934.73 seconds total)