Starting phenix.real_space_refine on Fri Mar 14 05:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymp_39402/03_2025/8ymp_39402_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymp_39402/03_2025/8ymp_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/cci-nas-00/data/ceres_data/8ymp_39402/03_2025/8ymp_39402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymp_39402/03_2025/8ymp_39402.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymp_39402/03_2025/8ymp_39402_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymp_39402/03_2025/8ymp_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-5624/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: 8.22, per 1000 atoms: 0.86 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 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: 1.02 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: 3.32 Time building geometry restraints manager: 3.19 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: 0.05 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: 0.010 Normalize map: mean=0, sd=1: 152.950 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.900 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 384 poor density : 229 time to evaluate : 0.973 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: 1.2825 time to fit residues: 700.5912 Evaluate side-chains 217 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 157 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.232887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191531 restraints weight = 13566.070| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.34 r_work: 0.4123 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 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 to be fit. rotamer outliers: 113 poor density : 142 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7207 (tt0) cc_final: 0.6964 (pt0) REVERT: A 215 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5334 (mt-10) REVERT: A 231 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8172 (p0) REVERT: A 238 VAL cc_start: 0.5548 (OUTLIER) cc_final: 0.5247 (p) REVERT: A 264 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6501 (pp) REVERT: A 310 ARG cc_start: 0.5999 (ttm170) cc_final: 0.5451 (mtp180) REVERT: A 352 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: A 379 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.3870 (mmp) REVERT: A 452 PHE cc_start: 0.6038 (t80) cc_final: 0.5837 (t80) REVERT: A 550 VAL cc_start: 0.0692 (OUTLIER) cc_final: 0.0282 (p) REVERT: A 658 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.4849 (t80) REVERT: B 182 GLU cc_start: 0.7212 (tt0) cc_final: 0.6968 (pt0) REVERT: B 215 GLU cc_start: 0.5618 (mt-10) cc_final: 0.5338 (mt-10) REVERT: B 231 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8157 (p0) REVERT: B 238 VAL cc_start: 0.5534 (OUTLIER) cc_final: 0.5234 (p) REVERT: B 264 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6502 (pp) REVERT: B 310 ARG cc_start: 0.5997 (ttm170) cc_final: 0.5450 (mtp180) REVERT: B 352 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: B 379 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.3858 (mmp) REVERT: B 550 VAL cc_start: 0.0694 (OUTLIER) cc_final: 0.0284 (p) REVERT: B 658 PHE cc_start: 0.5271 (OUTLIER) cc_final: 0.4873 (t80) outliers start: 113 outliers final: 28 residues processed: 228 average time/residue: 1.0245 time to fit residues: 254.0583 Evaluate side-chains 162 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 264 LEU 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 550 VAL 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 264 LEU 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 550 VAL 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 46 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 427 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.227004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.184910 restraints weight = 13678.269| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.23 r_work: 0.4088 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9828 Z= 0.220 Angle : 0.731 8.774 13360 Z= 0.366 Chirality : 0.044 0.174 1510 Planarity : 0.006 0.055 1664 Dihedral : 8.587 58.544 1342 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 7.63 % Allowed : 32.09 % 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: -0.41 (0.25), residues: 1168 helix: 0.92 (0.18), residues: 826 sheet: -3.53 (1.06), residues: 20 loop : -3.27 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 75 HIS 0.004 0.001 HIS B 74 PHE 0.017 0.002 PHE A 388 TYR 0.019 0.002 TYR A 713 ARG 0.006 0.001 ARG B 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 232 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 154 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7540 (tt0) cc_final: 0.7273 (pt0) REVERT: A 215 GLU cc_start: 0.5768 (mt-10) cc_final: 0.5214 (mp0) REVERT: A 231 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8025 (p0) REVERT: A 260 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5527 (m-30) REVERT: A 264 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6596 (pp) REVERT: A 352 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: A 379 MET cc_start: 0.5541 (mmt) cc_final: 0.4948 (mmm) REVERT: A 429 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5982 (pp) REVERT: A 472 PHE cc_start: 0.5733 (t80) cc_final: 0.5529 (t80) REVERT: A 479 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.4997 (pt) REVERT: A 550 VAL cc_start: 0.0736 (OUTLIER) cc_final: 0.0448 (p) REVERT: A 560 MET cc_start: 0.5768 (pp-130) cc_final: 0.3920 (mpp) REVERT: A 611 ILE cc_start: 0.6808 (pt) cc_final: 0.6473 (pt) REVERT: A 658 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.4835 (t80) REVERT: A 699 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.7163 (ttp80) REVERT: B 182 GLU cc_start: 0.7536 (tt0) cc_final: 0.7267 (pt0) REVERT: B 215 GLU cc_start: 0.5763 (mt-10) cc_final: 0.5207 (mp0) REVERT: B 231 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8018 (p0) REVERT: B 260 ASP cc_start: 0.5811 (OUTLIER) cc_final: 0.5527 (m-30) REVERT: B 264 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6599 (pp) REVERT: B 352 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: B 379 MET cc_start: 0.5563 (mmt) cc_final: 0.4965 (mmm) REVERT: B 429 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5985 (pp) REVERT: B 472 PHE cc_start: 0.5744 (t80) cc_final: 0.5490 (t80) REVERT: B 479 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4973 (pt) REVERT: B 550 VAL cc_start: 0.0737 (OUTLIER) cc_final: 0.0446 (p) REVERT: B 560 MET cc_start: 0.5772 (pp-130) cc_final: 0.3921 (mpp) REVERT: B 611 ILE cc_start: 0.6809 (pt) cc_final: 0.6474 (pt) REVERT: B 658 PHE cc_start: 0.5301 (OUTLIER) cc_final: 0.4815 (t80) REVERT: B 699 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.7159 (ttp80) outliers start: 78 outliers final: 17 residues processed: 213 average time/residue: 1.0259 time to fit residues: 236.6701 Evaluate side-chains 158 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 479 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 550 VAL 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 222 GLU Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 479 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 542 TYR Chi-restraints excluded: chain B residue 550 VAL 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 82 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.225583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.182035 restraints weight = 13384.085| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.30 r_work: 0.4038 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9828 Z= 0.213 Angle : 0.718 9.842 13360 Z= 0.353 Chirality : 0.044 0.227 1510 Planarity : 0.005 0.054 1664 Dihedral : 6.643 58.885 1312 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.48 % Allowed : 32.97 % Favored : 61.55 % 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: -0.11 (0.25), residues: 1168 helix: 1.18 (0.18), residues: 826 sheet: -4.23 (0.71), residues: 30 loop : -3.15 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 75 HIS 0.003 0.001 HIS A 90 PHE 0.030 0.002 PHE A 472 TYR 0.017 0.001 TYR B 713 ARG 0.005 0.001 ARG B 268 *********************** 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 198 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7406 (ttm) cc_final: 0.7135 (mtp) REVERT: A 102 TYR cc_start: 0.7172 (m-80) cc_final: 0.6952 (m-80) REVERT: A 182 GLU cc_start: 0.7606 (tt0) cc_final: 0.7318 (pt0) REVERT: A 215 GLU cc_start: 0.5775 (mt-10) cc_final: 0.5563 (mt-10) REVERT: A 352 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: A 379 MET cc_start: 0.5557 (mmt) cc_final: 0.5178 (mmm) REVERT: A 389 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.5706 (t80) REVERT: A 560 MET cc_start: 0.5705 (pp-130) cc_final: 0.3862 (mpp) REVERT: B 82 MET cc_start: 0.7422 (ttm) cc_final: 0.7150 (mtp) REVERT: B 102 TYR cc_start: 0.7168 (m-80) cc_final: 0.6939 (m-80) REVERT: B 182 GLU cc_start: 0.7606 (tt0) cc_final: 0.7318 (pt0) REVERT: B 215 GLU cc_start: 0.5769 (mt-10) cc_final: 0.5559 (mt-10) REVERT: B 352 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: B 379 MET cc_start: 0.5566 (mmt) cc_final: 0.5197 (mmm) REVERT: B 389 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5710 (t80) REVERT: B 560 MET cc_start: 0.5707 (pp-130) cc_final: 0.3863 (mpp) outliers start: 56 outliers final: 16 residues processed: 182 average time/residue: 0.9647 time to fit residues: 190.9534 Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN B 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.223781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.179900 restraints weight = 13318.148| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.30 r_work: 0.4013 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9828 Z= 0.223 Angle : 0.717 9.510 13360 Z= 0.354 Chirality : 0.044 0.316 1510 Planarity : 0.005 0.050 1664 Dihedral : 6.312 57.956 1304 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.09 % Allowed : 34.15 % Favored : 60.76 % 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: -0.07 (0.25), residues: 1168 helix: 1.21 (0.18), residues: 824 sheet: -4.18 (0.74), residues: 30 loop : -3.09 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 75 HIS 0.003 0.001 HIS B 90 PHE 0.031 0.002 PHE A 472 TYR 0.017 0.001 TYR B 713 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 5 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 198 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7656 (tt0) cc_final: 0.7352 (pt0) REVERT: A 215 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5459 (mt-10) REVERT: A 231 ASP cc_start: 0.8393 (p0) cc_final: 0.8154 (p0) REVERT: A 264 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6640 (pp) REVERT: A 305 GLU cc_start: 0.4394 (pt0) cc_final: 0.4042 (tp30) REVERT: A 352 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7369 (pm20) REVERT: A 389 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.5793 (t80) REVERT: A 429 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6057 (pp) REVERT: A 449 MET cc_start: 0.5830 (ptp) cc_final: 0.4856 (mtp) REVERT: A 464 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7669 (ttm-80) REVERT: A 560 MET cc_start: 0.5624 (pp-130) cc_final: 0.3806 (mpp) REVERT: A 565 ILE cc_start: 0.4749 (OUTLIER) cc_final: 0.4425 (pp) REVERT: B 176 MET cc_start: 0.8420 (mmm) cc_final: 0.8178 (mmm) REVERT: B 182 GLU cc_start: 0.7649 (tt0) cc_final: 0.7343 (pt0) REVERT: B 215 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5463 (mt-10) REVERT: B 231 ASP cc_start: 0.8391 (p0) cc_final: 0.8151 (p0) REVERT: B 264 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6636 (pp) REVERT: B 305 GLU cc_start: 0.4391 (pt0) cc_final: 0.4042 (tp30) REVERT: B 352 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: B 389 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.5797 (t80) REVERT: B 429 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6054 (pp) REVERT: B 464 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7646 (ttm-80) REVERT: B 524 ASP cc_start: 0.6195 (t0) cc_final: 0.5991 (t70) REVERT: B 560 MET cc_start: 0.5607 (pp-130) cc_final: 0.3797 (mpp) REVERT: B 565 ILE cc_start: 0.4775 (OUTLIER) cc_final: 0.4454 (pp) outliers start: 52 outliers final: 20 residues processed: 180 average time/residue: 1.2940 time to fit residues: 250.9539 Evaluate side-chains 168 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 464 ARG 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 519 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 464 ARG 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 519 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.222512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178344 restraints weight = 13247.027| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.29 r_work: 0.3993 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.8636 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= 0.234 Angle : 0.725 11.412 13360 Z= 0.354 Chirality : 0.044 0.358 1510 Planarity : 0.005 0.047 1664 Dihedral : 5.684 55.671 1298 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.87 % Allowed : 33.86 % 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: -0.05 (0.25), residues: 1168 helix: 1.15 (0.18), residues: 838 sheet: -3.88 (0.62), residues: 44 loop : -3.00 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 75 HIS 0.003 0.001 HIS A 90 PHE 0.037 0.002 PHE B 472 TYR 0.017 0.001 TYR A 713 ARG 0.004 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 6 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 207 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.5348 (mtt) cc_final: 0.4982 (ptp) REVERT: A 182 GLU cc_start: 0.7693 (tt0) cc_final: 0.7397 (pt0) REVERT: A 231 ASP cc_start: 0.8393 (p0) cc_final: 0.8092 (m-30) REVERT: A 264 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6651 (pp) REVERT: A 305 GLU cc_start: 0.4641 (pt0) cc_final: 0.4255 (tp30) REVERT: A 352 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: A 389 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6187 (m-10) REVERT: A 464 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7697 (ttm-80) REVERT: A 513 LYS cc_start: 0.4125 (OUTLIER) cc_final: 0.3412 (mtmm) REVERT: A 565 ILE cc_start: 0.4811 (OUTLIER) cc_final: 0.4554 (pp) REVERT: A 588 THR cc_start: 0.7371 (m) cc_final: 0.6626 (p) REVERT: B 114 MET cc_start: 0.5364 (mtt) cc_final: 0.4971 (ptp) REVERT: B 182 GLU cc_start: 0.7692 (tt0) cc_final: 0.7405 (pt0) REVERT: B 231 ASP cc_start: 0.8395 (p0) cc_final: 0.8092 (m-30) REVERT: B 264 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6648 (pp) REVERT: B 305 GLU cc_start: 0.4649 (pt0) cc_final: 0.4258 (tp30) REVERT: B 352 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: B 389 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.6165 (m-10) REVERT: B 464 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7690 (ttm-80) REVERT: B 513 LYS cc_start: 0.4126 (OUTLIER) cc_final: 0.3415 (mtmm) REVERT: B 565 ILE cc_start: 0.4789 (OUTLIER) cc_final: 0.4529 (pp) outliers start: 60 outliers final: 19 residues processed: 192 average time/residue: 1.1499 time to fit residues: 239.5013 Evaluate side-chains 166 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0181 > 50: distance: 74 - 94: 20.363 distance: 85 - 94: 18.314 distance: 94 - 95: 23.166 distance: 95 - 96: 28.311 distance: 95 - 98: 21.886 distance: 96 - 97: 12.883 distance: 96 - 99: 12.779 distance: 99 - 100: 11.087 distance: 99 - 105: 7.830 distance: 100 - 101: 7.632 distance: 100 - 103: 10.261 distance: 101 - 102: 19.993 distance: 101 - 106: 29.497 distance: 103 - 104: 15.028 distance: 104 - 105: 14.077 distance: 106 - 107: 12.061 distance: 107 - 108: 23.583 distance: 107 - 110: 39.934 distance: 108 - 109: 34.904 distance: 108 - 113: 27.665 distance: 110 - 111: 20.644 distance: 110 - 112: 15.833 distance: 113 - 114: 17.066 distance: 114 - 115: 33.772 distance: 114 - 117: 58.218 distance: 115 - 116: 29.307 distance: 115 - 120: 17.157 distance: 117 - 118: 27.660 distance: 117 - 119: 33.712 distance: 120 - 121: 28.389 distance: 120 - 126: 4.538 distance: 121 - 122: 19.080 distance: 121 - 124: 30.059 distance: 122 - 123: 16.477 distance: 122 - 127: 21.128 distance: 124 - 125: 14.531 distance: 125 - 126: 37.165 distance: 127 - 128: 17.871 distance: 128 - 129: 11.792 distance: 128 - 131: 17.007 distance: 129 - 130: 11.071 distance: 129 - 135: 11.737 distance: 131 - 132: 31.594 distance: 132 - 133: 13.594 distance: 133 - 134: 20.879 distance: 135 - 136: 18.543 distance: 136 - 137: 13.707 distance: 136 - 139: 11.752 distance: 137 - 138: 15.934 distance: 137 - 143: 13.650 distance: 138 - 169: 8.099 distance: 139 - 140: 14.800 distance: 140 - 141: 14.075 distance: 140 - 142: 17.550 distance: 143 - 144: 17.130 distance: 144 - 145: 15.666 distance: 144 - 147: 26.206 distance: 145 - 146: 9.683 distance: 145 - 151: 11.339 distance: 146 - 177: 9.277 distance: 147 - 148: 24.142 distance: 148 - 149: 14.037 distance: 148 - 150: 43.714 distance: 151 - 152: 4.359 distance: 151 - 157: 16.321 distance: 152 - 153: 6.370 distance: 152 - 155: 11.004 distance: 153 - 154: 10.418 distance: 153 - 158: 7.193 distance: 154 - 185: 19.736 distance: 155 - 156: 10.047 distance: 156 - 157: 23.052 distance: 158 - 159: 12.051 distance: 159 - 160: 15.271 distance: 159 - 162: 17.366 distance: 160 - 161: 9.893 distance: 160 - 169: 16.013 distance: 161 - 192: 28.588 distance: 162 - 163: 7.069 distance: 163 - 164: 4.512 distance: 163 - 165: 4.136 distance: 164 - 166: 10.717 distance: 165 - 167: 14.869 distance: 166 - 168: 20.644 distance: 167 - 168: 18.744