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/8cl4_16712.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl4_16712.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.14 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl4_16712.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl4_16712.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl4_16712.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8cl4_16712.pdb" } resolution = 3.14 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= 0.039 sd= 0.187 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 1393 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 23 5.16 5 C 1710 2.51 5 N 469 2.21 5 O 519 1.98 5 H 2719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5440 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1053 Classifications: {'peptide': 67} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1029 Classifications: {'peptide': 65} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3358 Inner-chain residues flagged as termini: ['pdbres="HIS A 87 "', 'pdbres="MET A 96 "'] Classifications: {'peptide': 213} Modifications used: {'COO': 2, 'NH2': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.18 Number of scatterers: 5440 At special positions: 0 Unit cell: (87.42, 74.4, 97.65, 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 23 16.00 O 519 8.00 N 469 7.00 C 1710 6.00 H 2719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.16 Conformation dependent library (CDL) restraints added in 164.0 milliseconds 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 66.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.803A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 removed outlier: 4.338A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.737A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.820A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 192 removed outlier: 4.282A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.710A pdb=" N ALA C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'A' and resid 17 through 30 removed outlier: 3.626A pdb=" N LYS A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Proline residue: A 38 - end of helix Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.324A pdb=" N THR A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 83 Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.669A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 161 through 174 removed outlier: 3.769A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 4.016A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.847A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 137 hydrogen bonds defined for protein. 399 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: 0.91 Time building geometry restraints manager: 1.33 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: 2713 1.15 - 1.31: 478 1.31 - 1.48: 1048 1.48 - 1.65: 1215 1.65 - 1.81: 40 Bond restraints: 5494 Sorted by residual: bond pdb=" ND1 HIS A 87 " pdb=" HD1 HIS A 87 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" N GLU A 98 " pdb=" H GLU A 98 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N THR A 186 " pdb=" H THR A 186 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N ALA A 42 " pdb=" H ALA A 42 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N HIS A 87 " pdb=" H HIS A 87 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 ... (remaining 5489 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.27: 116 106.27 - 113.19: 6567 113.19 - 120.12: 1655 120.12 - 127.04: 1592 127.04 - 133.96: 42 Bond angle restraints: 9972 Sorted by residual: angle pdb=" C VAL A 59 " pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 119.92 122.04 -2.12 9.60e-01 1.09e+00 4.88e+00 angle pdb=" C ARG A 97 " pdb=" N GLU A 98 " pdb=" CA GLU A 98 " ideal model delta sigma weight residual 120.49 117.97 2.52 1.42e+00 4.96e-01 3.15e+00 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 113.18 109.26 3.92 2.37e+00 1.78e-01 2.74e+00 angle pdb=" C PRO A 38 " pdb=" CA PRO A 38 " pdb=" CB PRO A 38 " ideal model delta sigma weight residual 113.20 110.42 2.78 1.69e+00 3.50e-01 2.71e+00 angle pdb=" CA LYS A 30 " pdb=" CB LYS A 30 " pdb=" CG LYS A 30 " ideal model delta sigma weight residual 114.10 111.10 3.00 2.00e+00 2.50e-01 2.25e+00 ... (remaining 9967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 2384 15.67 - 31.33: 130 31.33 - 47.00: 46 47.00 - 62.67: 22 62.67 - 78.34: 1 Dihedral angle restraints: 2583 sinusoidal: 1455 harmonic: 1128 Sorted by residual: dihedral pdb=" CA GLU C 175 " pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS A 62 " pdb=" C HIS A 62 " pdb=" N GLN A 63 " pdb=" CA GLN A 63 " ideal model delta harmonic sigma weight residual 180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLY A 61 " pdb=" C GLY A 61 " pdb=" N HIS A 62 " pdb=" CA HIS A 62 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 296 0.031 - 0.062: 81 0.062 - 0.093: 31 0.093 - 0.124: 10 0.124 - 0.155: 2 Chirality restraints: 420 Sorted by residual: chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 153 " pdb=" N ILE A 153 " pdb=" C ILE A 153 " pdb=" CB ILE A 153 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 417 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 186 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C THR C 186 " -0.031 2.00e-02 2.50e+03 pdb=" O THR C 186 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU C 187 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 186 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C THR A 186 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 186 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 187 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 195 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO B 196 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " 0.015 5.00e-02 4.00e+02 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 179 2.06 - 2.70: 7824 2.70 - 3.33: 16440 3.33 - 3.97: 19553 3.97 - 4.60: 29717 Nonbonded interactions: 73713 Sorted by model distance: nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.431 1.850 nonbonded pdb=" O ASN A 195 " pdb=" H LYS A 199 " model vdw 1.527 1.850 nonbonded pdb=" O ASN C 195 " pdb=" H LYS C 199 " model vdw 1.540 1.850 nonbonded pdb=" HG SER B 178 " pdb=" OE2 GLU A 180 " model vdw 1.593 1.850 nonbonded pdb=" O ILE A 153 " pdb="HD22 ASN A 193 " model vdw 1.606 1.850 ... (remaining 73708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 157 through 221) selection = (chain 'C' and ((resid 157 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3)) or resid 158 through 221)) } 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=0.49 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.100 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 7.180 Find NCS groups from input model: 0.050 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:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:4.160 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 0.044 2775 Z= 0.161 Angle : 0.528 3.921 3762 Z= 0.293 Chirality : 0.037 0.155 420 Planarity : 0.004 0.027 491 Dihedral : 10.485 78.336 1060 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.63 (0.41), residues: 337 helix: -0.52 (0.30), residues: 229 sheet: -1.96 (0.86), residues: 9 loop : 0.53 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 100 TYR 0.008 0.001 TYR B 169 PHE 0.002 0.001 PHE B 161 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.001 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.136 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 outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2049 time to fit residues: 31.5946 Evaluate side-chains 97 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2775 Z= 0.236 Angle : 0.539 3.915 3762 Z= 0.282 Chirality : 0.038 0.131 420 Planarity : 0.004 0.029 491 Dihedral : 6.213 79.757 369 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.35 % Allowed : 12.79 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.35 (0.43), residues: 337 helix: 0.19 (0.32), residues: 230 sheet: -1.99 (1.05), residues: 9 loop : 1.04 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.006 0.001 TYR A 130 PHE 0.010 0.001 PHE C 168 TRP 0.006 0.001 TRP A 133 HIS 0.001 0.001 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 MET cc_start: 0.8700 (mtm) cc_final: 0.8453 (mtm) REVERT: C 164 TYR cc_start: 0.8170 (t80) cc_final: 0.7502 (t80) REVERT: A 41 SER cc_start: 0.8793 (t) cc_final: 0.8253 (p) outliers start: 4 outliers final: 2 residues processed: 103 average time/residue: 0.3716 time to fit residues: 43.2245 Evaluate side-chains 98 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 68 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.7589 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2775 Z= 0.250 Angle : 0.532 4.015 3762 Z= 0.275 Chirality : 0.038 0.125 420 Planarity : 0.004 0.029 491 Dihedral : 6.303 87.622 369 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.01 % Allowed : 16.16 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.80 (0.44), residues: 337 helix: 0.56 (0.34), residues: 230 sheet: -2.21 (1.14), residues: 9 loop : 1.18 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.006 0.001 TYR A 130 PHE 0.006 0.001 PHE A 32 TRP 0.006 0.001 TRP A 184 HIS 0.001 0.000 HIS A 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 TYR cc_start: 0.8152 (t80) cc_final: 0.7433 (t80) REVERT: A 41 SER cc_start: 0.8865 (t) cc_final: 0.8155 (p) outliers start: 3 outliers final: 3 residues processed: 101 average time/residue: 0.2748 time to fit residues: 31.6686 Evaluate side-chains 97 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 68 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 GLN A 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2775 Z= 0.157 Angle : 0.501 4.101 3762 Z= 0.255 Chirality : 0.037 0.125 420 Planarity : 0.004 0.030 491 Dihedral : 5.898 81.561 369 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.01 % Allowed : 14.48 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.25 (0.45), residues: 337 helix: 0.96 (0.34), residues: 229 sheet: -2.19 (1.18), residues: 9 loop : 1.20 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.005 0.001 TYR A 169 PHE 0.018 0.001 PHE C 168 TRP 0.007 0.001 TRP A 184 HIS 0.001 0.000 HIS A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 TYR cc_start: 0.8089 (t80) cc_final: 0.7405 (t80) REVERT: A 41 SER cc_start: 0.8845 (t) cc_final: 0.8313 (p) outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.1931 time to fit residues: 22.0263 Evaluate side-chains 95 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2775 Z= 0.238 Angle : 0.546 5.649 3762 Z= 0.279 Chirality : 0.038 0.140 420 Planarity : 0.004 0.029 491 Dihedral : 5.561 72.655 369 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.34 % Allowed : 16.50 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.25 (0.45), residues: 337 helix: 0.98 (0.34), residues: 230 sheet: -2.31 (1.22), residues: 9 loop : 1.13 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 82 TYR 0.007 0.001 TYR A 169 PHE 0.014 0.001 PHE C 168 TRP 0.005 0.001 TRP C 184 HIS 0.001 0.000 HIS A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7626 (mm-30) REVERT: C 164 TYR cc_start: 0.8176 (t80) cc_final: 0.7433 (t80) REVERT: A 41 SER cc_start: 0.8864 (t) cc_final: 0.8205 (p) outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.1606 time to fit residues: 18.8836 Evaluate side-chains 96 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN A 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2775 Z= 0.189 Angle : 0.535 5.046 3762 Z= 0.274 Chirality : 0.038 0.152 420 Planarity : 0.004 0.035 491 Dihedral : 5.387 68.482 369 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.67 % Allowed : 17.17 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.46 (0.45), residues: 337 helix: 1.19 (0.34), residues: 229 sheet: -2.38 (1.20), residues: 9 loop : 1.13 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.005 0.001 TYR A 169 PHE 0.014 0.001 PHE C 168 TRP 0.007 0.001 TRP C 184 HIS 0.001 0.000 HIS A 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 620.75 seconds wall clock time: 11 minutes 6.15 seconds (666.15 seconds total)