Starting phenix.real_space_refine (version: dev) on Thu Feb 16 15:25:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/02_2023/5m5h_4155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/02_2023/5m5h_4155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/02_2023/5m5h_4155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/02_2023/5m5h_4155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/02_2023/5m5h_4155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/02_2023/5m5h_4155.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 1086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1086 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.29, per 1000 atoms: 1.19 Number of scatterers: 1086 At special positions: 0 Unit cell: (54.2, 49.864, 54.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 164 8.00 N 157 7.00 C 757 6.00 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: 0.45 Conformation dependent library (CDL) restraints added in 179.9 milliseconds 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 252 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 68.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 425 through 428 removed outlier: 3.881A pdb=" N ILE A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.714A pdb=" N ILE A 469 " --> pdb=" O TYR A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 removed outlier: 3.501A pdb=" N THR A 496 " --> pdb=" O LYS A 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.510A pdb=" N ILE A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 527 removed outlier: 3.932A pdb=" N VAL A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) 55 hydrogen bonds defined for protein. 165 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: 0.25 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 240 1.34 - 1.46: 290 1.46 - 1.58: 581 1.58 - 1.70: 0 1.70 - 1.82: 15 Bond restraints: 1126 Sorted by residual: bond pdb=" C MET A 498 " pdb=" O MET A 498 " ideal model delta sigma weight residual 1.238 1.222 0.016 9.50e-03 1.11e+04 2.79e+00 bond pdb=" CA VAL A 351 " pdb=" C VAL A 351 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.31e-02 5.83e+03 2.58e+00 bond pdb=" CA TYR A 465 " pdb=" C TYR A 465 " ideal model delta sigma weight residual 1.525 1.547 -0.021 1.40e-02 5.10e+03 2.30e+00 bond pdb=" C PHE A 502 " pdb=" O PHE A 502 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.15e-02 7.56e+03 2.03e+00 bond pdb=" N PHE A 424 " pdb=" CA PHE A 424 " ideal model delta sigma weight residual 1.465 1.451 0.014 1.05e-02 9.07e+03 1.75e+00 ... (remaining 1121 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.20: 36 105.20 - 112.45: 521 112.45 - 119.70: 429 119.70 - 126.94: 527 126.94 - 134.19: 24 Bond angle restraints: 1537 Sorted by residual: angle pdb=" C TRP A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta sigma weight residual 122.26 114.49 7.77 1.59e+00 3.96e-01 2.39e+01 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 113.18 124.74 -11.56 2.37e+00 1.78e-01 2.38e+01 angle pdb=" C CYS A 423 " pdb=" N PHE A 424 " pdb=" CA PHE A 424 " ideal model delta sigma weight residual 122.28 117.93 4.35 1.02e+00 9.61e-01 1.82e+01 angle pdb=" CA TYR A 464 " pdb=" CB TYR A 464 " pdb=" CG TYR A 464 " ideal model delta sigma weight residual 113.90 121.19 -7.29 1.80e+00 3.09e-01 1.64e+01 angle pdb=" C PHE A 497 " pdb=" N MET A 498 " pdb=" CA MET A 498 " ideal model delta sigma weight residual 121.62 127.11 -5.49 1.57e+00 4.06e-01 1.22e+01 ... (remaining 1532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.25: 467 8.25 - 16.50: 103 16.50 - 24.75: 40 24.75 - 33.00: 10 33.00 - 41.25: 12 Dihedral angle restraints: 632 sinusoidal: 244 harmonic: 388 Sorted by residual: dihedral pdb=" CA PHE A 424 " pdb=" C PHE A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 141.50 38.50 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA VAL A 351 " pdb=" C VAL A 351 " pdb=" N GLY A 352 " pdb=" CA GLY A 352 " ideal model delta harmonic sigma weight residual -180.00 -143.11 -36.89 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA GLN A 527 " pdb=" C GLN A 527 " pdb=" N GLN A 528 " pdb=" CA GLN A 528 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 90 0.047 - 0.094: 53 0.094 - 0.141: 17 0.141 - 0.188: 10 0.188 - 0.235: 4 Chirality restraints: 174 Sorted by residual: chirality pdb=" CG LEU A 446 " pdb=" CB LEU A 446 " pdb=" CD1 LEU A 446 " pdb=" CD2 LEU A 446 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LEU A 446 " pdb=" N LEU A 446 " pdb=" C LEU A 446 " pdb=" CB LEU A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 171 not shown) Planarity restraints: 180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " -0.032 2.00e-02 2.50e+03 2.14e-02 9.15e+00 pdb=" CG TYR A 517 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 467 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 468 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 424 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 425 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.036 5.00e-02 4.00e+02 ... (remaining 177 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 107 2.73 - 3.27: 1132 3.27 - 3.81: 1718 3.81 - 4.36: 2184 4.36 - 4.90: 3185 Nonbonded interactions: 8326 Sorted by model distance: nonbonded pdb=" O MET A 498 " pdb=" N ILE A 501 " model vdw 2.186 2.520 nonbonded pdb=" O LEU A 344 " pdb=" ND1 HIS A 348 " model vdw 2.310 2.520 nonbonded pdb=" O PHE A 506 " pdb=" N PHE A 509 " model vdw 2.361 2.520 nonbonded pdb=" O ILE A 364 " pdb=" N GLY A 367 " model vdw 2.381 2.520 nonbonded pdb=" O LEU A 426 " pdb=" N GLN A 429 " model vdw 2.384 2.520 ... (remaining 8321 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 757 2.51 5 N 157 2.21 5 O 164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.690 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: 0.000 Extract box with map and model: 17.610 Check model and map are aligned: 0.020 Process input model: 11.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1430 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 : 0.007 0.044 1126 Z= 0.465 Angle : 1.499 11.564 1537 Z= 0.831 Chirality : 0.075 0.235 174 Planarity : 0.011 0.067 180 Dihedral : 12.373 41.255 380 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 39.89 Ramachandran Plot: Outliers : 2.38 % Allowed : 8.73 % Favored : 88.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % Twisted Proline : 11.11 % Twisted General : 0.83 % 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: -5.94 (0.48), residues: 126 helix: -3.97 (0.37), residues: 70 sheet: None (None), residues: 0 loop : -3.84 (0.60), residues: 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0882 time to fit residues: 2.4582 Evaluate side-chains 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.0670 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 overall best weight: 3.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1360 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 1126 Z= 0.232 Angle : 0.918 7.729 1537 Z= 0.471 Chirality : 0.053 0.156 174 Planarity : 0.009 0.059 180 Dihedral : 8.315 28.407 138 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -3.74 (0.62), residues: 126 helix: -1.95 (0.48), residues: 78 sheet: None (None), residues: 0 loop : -3.26 (0.80), residues: 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.123 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0783 time to fit residues: 1.9689 Evaluate side-chains 14 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 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 521 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1369 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 1126 Z= 0.247 Angle : 0.905 6.182 1537 Z= 0.464 Chirality : 0.055 0.201 174 Planarity : 0.009 0.069 180 Dihedral : 8.111 29.868 138 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 1.59 % Allowed : 8.73 % Favored : 89.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -3.12 (0.68), residues: 126 helix: -1.32 (0.52), residues: 81 sheet: None (None), residues: 0 loop : -3.41 (0.85), residues: 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0740 time to fit residues: 1.8614 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 7 optimal weight: 0.0270 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.7844 ------------------------------------------------------------------------------- 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: 0.1313 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 1126 Z= 0.211 Angle : 0.847 7.427 1537 Z= 0.426 Chirality : 0.052 0.192 174 Planarity : 0.009 0.058 180 Dihedral : 7.044 23.477 138 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -2.73 (0.67), residues: 126 helix: -0.92 (0.51), residues: 78 sheet: None (None), residues: 0 loop : -3.32 (0.85), residues: 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0862 time to fit residues: 1.7351 Evaluate side-chains 13 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.0970 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 overall best weight: 4.3784 ------------------------------------------------------------------------------- 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: 0.1312 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 1126 Z= 0.216 Angle : 0.838 7.306 1537 Z= 0.422 Chirality : 0.052 0.213 174 Planarity : 0.009 0.064 180 Dihedral : 6.752 22.097 138 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -2.58 (0.66), residues: 126 helix: -0.65 (0.51), residues: 79 sheet: None (None), residues: 0 loop : -3.61 (0.77), residues: 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.130 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1031 time to fit residues: 2.1311 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 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: 0.1314 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 1126 Z= 0.237 Angle : 0.886 7.931 1537 Z= 0.439 Chirality : 0.054 0.202 174 Planarity : 0.008 0.049 180 Dihedral : 6.676 20.538 138 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -2.37 (0.66), residues: 126 helix: -0.50 (0.52), residues: 82 sheet: None (None), residues: 0 loop : -3.68 (0.74), residues: 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0680 time to fit residues: 1.4865 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 0.0050 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1269 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 1126 Z= 0.185 Angle : 0.799 8.086 1537 Z= 0.388 Chirality : 0.051 0.189 174 Planarity : 0.008 0.056 180 Dihedral : 6.268 20.769 138 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.56 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.87 (0.67), residues: 126 helix: -0.04 (0.53), residues: 82 sheet: None (None), residues: 0 loop : -3.63 (0.70), residues: 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.124 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0792 time to fit residues: 1.7327 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.0070 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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: 0.1255 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 1126 Z= 0.202 Angle : 0.814 8.602 1537 Z= 0.403 Chirality : 0.052 0.216 174 Planarity : 0.008 0.046 180 Dihedral : 6.113 20.398 138 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.64 (0.69), residues: 126 helix: 0.13 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -3.53 (0.70), residues: 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0686 time to fit residues: 1.5218 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.0010 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.1392 ------------------------------------------------------------------------------- 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: 0.1263 moved from start: 0.8037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 1126 Z= 0.185 Angle : 0.778 9.074 1537 Z= 0.375 Chirality : 0.051 0.216 174 Planarity : 0.008 0.046 180 Dihedral : 6.004 20.982 138 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.30 (0.70), residues: 126 helix: 0.40 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -3.43 (0.72), residues: 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0798 time to fit residues: 1.9116 Evaluate side-chains 14 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 overall best weight: 6.2146 ------------------------------------------------------------------------------- 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: 0.1307 moved from start: 0.8125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 1126 Z= 0.256 Angle : 0.863 8.304 1537 Z= 0.441 Chirality : 0.052 0.149 174 Planarity : 0.008 0.047 180 Dihedral : 6.344 22.234 138 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.51 (0.70), residues: 126 helix: 0.22 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -3.45 (0.73), residues: 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0841 time to fit residues: 1.7073 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9857 > 50: distance: 33 - 35: 15.589 distance: 35 - 36: 9.918 distance: 36 - 37: 19.864 distance: 36 - 39: 10.275 distance: 37 - 38: 10.289 distance: 37 - 41: 4.945 distance: 39 - 40: 22.780 distance: 41 - 42: 7.033 distance: 42 - 43: 9.507 distance: 42 - 45: 5.857 distance: 43 - 44: 6.282 distance: 43 - 48: 7.117 distance: 45 - 46: 12.400 distance: 45 - 47: 6.879 distance: 48 - 49: 4.427 distance: 49 - 50: 3.447 distance: 50 - 51: 19.024 distance: 50 - 57: 17.638 distance: 52 - 53: 3.611 distance: 53 - 54: 3.505 distance: 54 - 55: 3.819 distance: 57 - 58: 12.073 distance: 58 - 59: 10.865 distance: 58 - 61: 7.615 distance: 59 - 60: 31.492 distance: 59 - 65: 29.059 distance: 61 - 62: 5.150 distance: 62 - 63: 14.213 distance: 62 - 64: 14.280 distance: 65 - 66: 16.831 distance: 66 - 67: 25.742 distance: 66 - 69: 12.930 distance: 67 - 68: 10.313 distance: 67 - 76: 9.603 distance: 69 - 70: 11.814 distance: 70 - 71: 3.620 distance: 71 - 72: 9.959 distance: 73 - 75: 6.980 distance: 76 - 77: 5.561 distance: 77 - 78: 4.905 distance: 77 - 80: 4.038 distance: 78 - 79: 11.204 distance: 78 - 85: 4.117 distance: 80 - 81: 4.568 distance: 81 - 82: 5.237 distance: 82 - 83: 6.627 distance: 82 - 84: 9.191 distance: 85 - 86: 10.988 distance: 86 - 87: 7.272 distance: 86 - 89: 7.205 distance: 87 - 88: 12.552 distance: 87 - 90: 9.852 distance: 90 - 91: 6.010 distance: 90 - 96: 10.300 distance: 91 - 92: 7.391 distance: 91 - 94: 6.767 distance: 92 - 93: 3.622 distance: 94 - 95: 10.283 distance: 95 - 96: 7.171 distance: 97 - 98: 3.047 distance: 98 - 99: 7.298 distance: 99 - 100: 10.380 distance: 99 - 108: 6.410 distance: 101 - 102: 3.208 distance: 102 - 103: 3.537 distance: 102 - 104: 9.543 distance: 103 - 105: 4.751 distance: 104 - 106: 5.277 distance: 105 - 107: 8.352 distance: 106 - 107: 5.454 distance: 109 - 110: 11.076 distance: 109 - 112: 9.893 distance: 110 - 111: 20.165 distance: 110 - 113: 12.039