Starting phenix.real_space_refine on Fri Oct 11 09:35:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymp_39402/10_2024/8ymp_39402_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymp_39402/10_2024/8ymp_39402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymp_39402/10_2024/8ymp_39402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymp_39402/10_2024/8ymp_39402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymp_39402/10_2024/8ymp_39402_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ymp_39402/10_2024/8ymp_39402_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6316 2.51 5 N 1560 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4776 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 32, 'TRANS': 559} Chain breaks: 3 Chain: "B" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4776 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 32, 'TRANS': 559} Chain breaks: 3 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 8.98, per 1000 atoms: 0.94 Number of scatterers: 9570 At special positions: 0 Unit cell: (149.91, 90.63, 94.62, 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 50 16.00 O 1644 8.00 N 1560 7.00 C 6316 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 74.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 68 through 81 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.664A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 160 through 194 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 265 removed outlier: 3.750A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.889A pdb=" N TYR A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 368 through 408 removed outlier: 4.607A pdb=" N THR A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 434 through 454 Proline residue: A 443 - end of helix removed outlier: 3.838A pdb=" N MET A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 478 Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 536 through 549 Processing helix chain 'A' and resid 569 through 585 Processing helix chain 'A' and resid 590 through 613 removed outlier: 3.681A pdb=" N PHE A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 647 removed outlier: 3.669A pdb=" N GLY A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 677 removed outlier: 3.561A pdb=" N ALA A 661 " --> pdb=" O PRO A 657 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Proline residue: A 663 - end of helix Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 705 through 711 removed outlier: 3.947A pdb=" N ASP A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 92 through 107 removed outlier: 3.664A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 160 through 194 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 242 through 265 removed outlier: 3.750A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.889A pdb=" N TYR B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 368 through 408 removed outlier: 4.607A pdb=" N THR B 373 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 423 through 433 Processing helix chain 'B' and resid 434 through 454 Proline residue: B 443 - end of helix removed outlier: 3.838A pdb=" N MET B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 478 Processing helix chain 'B' and resid 481 through 498 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 590 through 613 removed outlier: 3.681A pdb=" N PHE B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 647 removed outlier: 3.669A pdb=" N GLY B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 677 removed outlier: 3.561A pdb=" N ALA B 661 " --> pdb=" O PRO B 657 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 662 " --> pdb=" O PHE B 658 " (cutoff:3.500A) Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 705 through 711 removed outlier: 3.947A pdb=" N ASP B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 207 Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 235 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 240 removed outlier: 5.096A pdb=" N VAL A 239 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 204 through 207 Processing sheet with id=AA5, first strand: chain 'B' and resid 233 through 235 Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 240 removed outlier: 5.096A pdb=" N VAL B 239 " --> pdb=" O MET B 321 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1773 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: 2.74 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1480 1.29 - 1.42: 2650 1.42 - 1.55: 5590 1.55 - 1.68: 20 1.68 - 1.81: 88 Bond restraints: 9828 Sorted by residual: bond pdb=" C ILE B 433 " pdb=" O ILE B 433 " ideal model delta sigma weight residual 1.236 1.158 0.078 1.19e-02 7.06e+03 4.27e+01 bond pdb=" C ILE A 433 " pdb=" O ILE A 433 " ideal model delta sigma weight residual 1.236 1.158 0.078 1.19e-02 7.06e+03 4.27e+01 bond pdb=" C MET B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.335 1.386 -0.051 9.40e-03 1.13e+04 2.95e+01 bond pdb=" C MET A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.335 1.386 -0.051 9.40e-03 1.13e+04 2.95e+01 bond pdb=" CA PRO B 443 " pdb=" C PRO B 443 " ideal model delta sigma weight residual 1.520 1.455 0.065 1.42e-02 4.96e+03 2.07e+01 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.42: 13220 5.42 - 10.83: 120 10.83 - 16.25: 16 16.25 - 21.66: 2 21.66 - 27.08: 2 Bond angle restraints: 13360 Sorted by residual: angle pdb=" C MET B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 120.45 102.99 17.46 1.11e+00 8.12e-01 2.47e+02 angle pdb=" C MET A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta sigma weight residual 120.45 102.99 17.46 1.11e+00 8.12e-01 2.47e+02 angle pdb=" N ILE B 440 " pdb=" CA ILE B 440 " pdb=" C ILE B 440 " ideal model delta sigma weight residual 110.30 98.01 12.29 9.70e-01 1.06e+00 1.61e+02 angle pdb=" N ILE A 440 " pdb=" CA ILE A 440 " pdb=" C ILE A 440 " ideal model delta sigma weight residual 110.30 98.01 12.29 9.70e-01 1.06e+00 1.61e+02 angle pdb=" N ASP A 260 " pdb=" CA ASP A 260 " pdb=" C ASP A 260 " ideal model delta sigma weight residual 112.90 99.48 13.42 1.31e+00 5.83e-01 1.05e+02 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4524 17.71 - 35.41: 562 35.41 - 53.12: 496 53.12 - 70.82: 206 70.82 - 88.53: 26 Dihedral angle restraints: 5814 sinusoidal: 2318 harmonic: 3496 Sorted by residual: dihedral pdb=" N LEU A 549 " pdb=" C LEU A 549 " pdb=" CA LEU A 549 " pdb=" CB LEU A 549 " ideal model delta harmonic sigma weight residual 122.80 137.73 -14.93 0 2.50e+00 1.60e-01 3.57e+01 dihedral pdb=" N LEU B 549 " pdb=" C LEU B 549 " pdb=" CA LEU B 549 " pdb=" CB LEU B 549 " ideal model delta harmonic sigma weight residual 122.80 137.73 -14.93 0 2.50e+00 1.60e-01 3.57e+01 dihedral pdb=" C LEU A 549 " pdb=" N LEU A 549 " pdb=" CA LEU A 549 " pdb=" CB LEU A 549 " ideal model delta harmonic sigma weight residual -122.60 -136.71 14.11 0 2.50e+00 1.60e-01 3.19e+01 ... (remaining 5811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1374 0.148 - 0.296: 116 0.296 - 0.443: 14 0.443 - 0.591: 4 0.591 - 0.739: 2 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA LEU A 549 " pdb=" N LEU A 549 " pdb=" C LEU A 549 " pdb=" CB LEU A 549 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA LEU B 549 " pdb=" N LEU B 549 " pdb=" C LEU B 549 " pdb=" CB LEU B 549 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA MET B 76 " pdb=" N MET B 76 " pdb=" C MET B 76 " pdb=" CB MET B 76 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.29e+00 ... (remaining 1507 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 498 " -0.119 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO A 499 " 0.313 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " -0.103 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 498 " 0.119 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO B 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 442 " 0.097 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO B 443 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO B 443 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 443 " 0.081 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 184 2.63 - 3.19: 8706 3.19 - 3.76: 16285 3.76 - 4.33: 22808 4.33 - 4.90: 34575 Nonbonded interactions: 82558 Sorted by model distance: nonbonded pdb=" O ARG B 358 " pdb=" CG ARG B 358 " model vdw 2.057 3.440 nonbonded pdb=" O ARG A 358 " pdb=" CG ARG A 358 " model vdw 2.057 3.440 nonbonded pdb=" O ILE A 433 " pdb=" N LYS A 436 " model vdw 2.272 3.120 nonbonded pdb=" O ILE B 433 " pdb=" N LYS B 436 " model vdw 2.272 3.120 nonbonded pdb=" O ILE A 433 " pdb=" N LEU A 435 " model vdw 2.330 3.120 ... (remaining 82553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 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 individual isotropic 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: 18.660 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.830 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4922 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 : 0.008 0.078 9828 Z= 0.508 Angle : 1.418 27.079 13360 Z= 0.925 Chirality : 0.094 0.739 1510 Planarity : 0.011 0.181 1664 Dihedral : 25.414 88.526 3546 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 2.23 % Allowed : 10.62 % Favored : 87.16 % Rotamer: Outliers : 37.57 % Allowed : 13.70 % Favored : 48.73 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 0.00 % 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: -3.93 (0.19), residues: 1168 helix: -1.78 (0.15), residues: 808 sheet: None (None), residues: 0 loop : -4.38 (0.23), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 75 HIS 0.003 0.001 HIS B 629 PHE 0.026 0.002 PHE B 472 TYR 0.012 0.001 TYR B 713 ARG 0.001 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 229 time to evaluate : 1.171 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: A 231 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5264 (p0) REVERT: A 481 SER cc_start: 0.4253 (OUTLIER) cc_final: 0.3727 (p) REVERT: B 231 ASP cc_start: 0.5730 (OUTLIER) cc_final: 0.5267 (p0) REVERT: B 481 SER cc_start: 0.4255 (OUTLIER) cc_final: 0.3743 (p) outliers start: 384 outliers final: 56 residues processed: 505 average time/residue: 1.0605 time to fit residues: 578.5290 Evaluate side-chains 217 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 157 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 703 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.0060 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 228 ASN A 263 GLN A 269 ASN A 294 HIS A 339 GLN A 398 GLN A 490 GLN A 543 HIS ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 575 GLN B 208 ASN B 228 ASN B 263 GLN B 269 ASN B 294 HIS B 315 ASN B 339 GLN B 398 GLN B 490 GLN B 546 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 575 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9828 Z= 0.247 Angle : 0.807 12.501 13360 Z= 0.404 Chirality : 0.046 0.213 1510 Planarity : 0.007 0.056 1664 Dihedral : 10.506 59.335 1396 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 11.06 % Allowed : 28.96 % Favored : 59.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.24), residues: 1168 helix: 0.09 (0.18), residues: 822 sheet: -4.10 (0.92), residues: 20 loop : -3.69 (0.28), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 75 HIS 0.006 0.002 HIS B 74 PHE 0.024 0.002 PHE B 472 TYR 0.025 0.002 TYR A 295 ARG 0.007 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 142 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.5608 (OUTLIER) cc_final: 0.5362 (p0) REVERT: A 238 VAL cc_start: 0.6225 (OUTLIER) cc_final: 0.5949 (p) REVERT: A 352 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5237 (pt0) REVERT: A 379 MET cc_start: 0.3680 (OUTLIER) cc_final: 0.2679 (mmp) REVERT: A 658 PHE cc_start: 0.4068 (OUTLIER) cc_final: 0.3689 (t80) REVERT: B 231 ASP cc_start: 0.5616 (OUTLIER) cc_final: 0.5384 (p0) REVERT: B 238 VAL cc_start: 0.6226 (OUTLIER) cc_final: 0.5940 (p) REVERT: B 352 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.5240 (pt0) REVERT: B 379 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.2687 (mmp) REVERT: B 658 PHE cc_start: 0.4139 (OUTLIER) cc_final: 0.3732 (t80) outliers start: 113 outliers final: 28 residues processed: 228 average time/residue: 0.9751 time to fit residues: 242.7256 Evaluate side-chains 154 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 95 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 287 GLN A 312 ASN A 546 ASN A 561 ASN B 162 HIS B 287 GLN B 312 ASN B 427 GLN B 561 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9828 Z= 0.215 Angle : 0.734 9.623 13360 Z= 0.366 Chirality : 0.044 0.179 1510 Planarity : 0.006 0.055 1664 Dihedral : 8.457 58.927 1340 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 7.14 % Allowed : 32.58 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.25), residues: 1168 helix: 0.93 (0.18), residues: 828 sheet: -3.61 (1.02), residues: 20 loop : -3.26 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 75 HIS 0.007 0.001 HIS A 223 PHE 0.017 0.002 PHE A 388 TYR 0.020 0.002 TYR A 713 ARG 0.005 0.001 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 150 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5354 (pm20) REVERT: A 379 MET cc_start: 0.4138 (mmt) cc_final: 0.3636 (mmm) REVERT: A 429 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5759 (pp) REVERT: A 472 PHE cc_start: 0.4473 (t80) cc_final: 0.4088 (t80) REVERT: A 560 MET cc_start: 0.4289 (pp-130) cc_final: 0.3452 (mpp) REVERT: A 611 ILE cc_start: 0.5769 (pt) cc_final: 0.5252 (pt) REVERT: A 658 PHE cc_start: 0.4084 (OUTLIER) cc_final: 0.3509 (t80) REVERT: B 352 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5342 (pm20) REVERT: B 379 MET cc_start: 0.4161 (mmt) cc_final: 0.3659 (mmm) REVERT: B 429 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5731 (pp) REVERT: B 472 PHE cc_start: 0.4477 (t80) cc_final: 0.4093 (t80) REVERT: B 560 MET cc_start: 0.4282 (pp-130) cc_final: 0.3442 (mpp) REVERT: B 611 ILE cc_start: 0.5786 (pt) cc_final: 0.5254 (pt) REVERT: B 658 PHE cc_start: 0.4084 (OUTLIER) cc_final: 0.3514 (t80) outliers start: 73 outliers final: 18 residues processed: 202 average time/residue: 1.0554 time to fit residues: 230.6399 Evaluate side-chains 140 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 0.0870 chunk 30 optimal weight: 6.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 315 ASN A 568 ASN A 616 GLN B 243 ASN B 568 ASN B 616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.7590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9828 Z= 0.196 Angle : 0.713 9.755 13360 Z= 0.346 Chirality : 0.043 0.213 1510 Planarity : 0.005 0.054 1664 Dihedral : 6.494 57.502 1308 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.60 % Allowed : 33.66 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.26), residues: 1168 helix: 1.24 (0.18), residues: 828 sheet: -4.31 (0.67), residues: 30 loop : -3.10 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 75 HIS 0.002 0.001 HIS B 90 PHE 0.029 0.002 PHE B 472 TYR 0.017 0.001 TYR A 713 ARG 0.004 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 134 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.6466 (m-80) cc_final: 0.6081 (m-80) REVERT: A 352 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5376 (pm20) REVERT: A 379 MET cc_start: 0.4298 (mmt) cc_final: 0.3633 (mmm) REVERT: A 389 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.4293 (t80) REVERT: A 560 MET cc_start: 0.4270 (pp-130) cc_final: 0.3530 (mpp) REVERT: A 611 ILE cc_start: 0.5772 (pt) cc_final: 0.5273 (pt) REVERT: B 102 TYR cc_start: 0.6485 (m-80) cc_final: 0.6085 (m-80) REVERT: B 352 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5372 (pm20) REVERT: B 379 MET cc_start: 0.4305 (mmt) cc_final: 0.3627 (mmm) REVERT: B 389 PHE cc_start: 0.4898 (OUTLIER) cc_final: 0.4297 (t80) REVERT: B 560 MET cc_start: 0.4267 (pp-130) cc_final: 0.3521 (mpp) REVERT: B 611 ILE cc_start: 0.5793 (pt) cc_final: 0.5280 (pt) outliers start: 47 outliers final: 18 residues processed: 166 average time/residue: 0.9428 time to fit residues: 170.9262 Evaluate side-chains 145 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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-5477/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-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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: 62.144 > 50: distance: 16 - 20: 19.112 distance: 17 - 41: 16.969 distance: 20 - 21: 10.019 distance: 20 - 26: 38.678 distance: 21 - 22: 24.111 distance: 21 - 24: 19.314 distance: 22 - 23: 52.792 distance: 22 - 27: 33.150 distance: 23 - 49: 24.697 distance: 25 - 26: 59.588 distance: 27 - 28: 19.225 distance: 28 - 29: 13.772 distance: 28 - 31: 26.777 distance: 29 - 30: 14.595 distance: 29 - 36: 15.279 distance: 31 - 32: 12.706 distance: 32 - 33: 5.168 distance: 33 - 35: 9.686 distance: 36 - 37: 13.539 distance: 37 - 38: 28.425 distance: 37 - 40: 34.518 distance: 38 - 39: 7.456 distance: 38 - 41: 38.865 distance: 41 - 42: 15.778 distance: 42 - 43: 35.969 distance: 42 - 45: 9.588 distance: 43 - 44: 25.262 distance: 43 - 49: 7.905 distance: 45 - 46: 7.754 distance: 46 - 47: 25.539 distance: 46 - 48: 10.533 distance: 49 - 50: 16.086 distance: 50 - 51: 36.291 distance: 50 - 53: 25.473 distance: 51 - 52: 20.059 distance: 51 - 58: 28.902 distance: 53 - 54: 25.807 distance: 54 - 55: 7.026 distance: 55 - 56: 7.353 distance: 56 - 57: 5.862 distance: 58 - 59: 21.499 distance: 59 - 60: 11.139 distance: 59 - 62: 42.109 distance: 60 - 61: 4.248 distance: 60 - 66: 30.524 distance: 62 - 63: 35.151 distance: 63 - 64: 7.434 distance: 64 - 65: 51.354 distance: 66 - 67: 23.959 distance: 66 - 72: 38.212 distance: 67 - 68: 54.163 distance: 67 - 70: 37.183 distance: 68 - 69: 9.955 distance: 68 - 73: 8.329 distance: 70 - 71: 11.364 distance: 71 - 72: 29.967 distance: 73 - 74: 30.037 distance: 74 - 75: 18.273 distance: 74 - 77: 19.013 distance: 75 - 76: 14.856 distance: 75 - 82: 17.388 distance: 76 - 110: 19.019 distance: 77 - 78: 31.718 distance: 78 - 79: 14.099 distance: 79 - 80: 18.024 distance: 79 - 81: 32.609 distance: 83 - 84: 21.619 distance: 83 - 86: 13.863 distance: 84 - 85: 5.740 distance: 85 - 118: 18.125 distance: 86 - 87: 13.212 distance: 87 - 88: 31.281 distance: 88 - 89: 18.226 distance: 89 - 90: 28.714 distance: 90 - 91: 20.110 distance: 90 - 92: 14.417 distance: 93 - 94: 13.557 distance: 94 - 95: 4.531 distance: 94 - 97: 3.939 distance: 95 - 96: 7.324 distance: 95 - 102: 16.677 distance: 96 - 126: 25.350 distance: 97 - 98: 17.278 distance: 98 - 99: 10.368 distance: 99 - 100: 10.085 distance: 99 - 101: 34.723