Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 21:34:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/10_2023/7rr6_24653_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/10_2023/7rr6_24653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/10_2023/7rr6_24653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/10_2023/7rr6_24653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/10_2023/7rr6_24653_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rr6_24653/10_2023/7rr6_24653_updated.pdb" } resolution = 3.1 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= 0.019 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 132 5.16 5 C 15413 2.51 5 N 3824 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 947": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 23821 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7756 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 976} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7752 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 976} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7658 Classifications: {'peptide': 1019} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 973} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 197 Unusual residues: {'D12': 4, 'PTY': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PTY:plan-1': 5, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Unusual residues: {'D12': 4, 'PTY': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-1': 2, 'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Unusual residues: {'PTY': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PTY:plan-1': 5, 'PTY:plan-2': 5} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 12.10, per 1000 atoms: 0.51 Number of scatterers: 23821 At special positions: 0 Unit cell: (121.049, 115.124, 145.598, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 15 15.00 O 4437 8.00 N 3824 7.00 C 15413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.72 Conformation dependent library (CDL) restraints added in 3.5 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 24 sheets defined 51.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 100 through 117 Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.508A pdb=" N TYR B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.685A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.336A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 4.141A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 456 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 462 through 486 removed outlier: 3.610A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.577A pdb=" N ARG B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 557 removed outlier: 3.797A pdb=" N LEU B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 600 Processing helix chain 'B' and resid 644 through 657 removed outlier: 4.236A pdb=" N GLN B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 708 removed outlier: 3.684A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 743 through 754 Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 783 through 788 Processing helix chain 'B' and resid 801 through 804 No H-bonds generated for 'chain 'B' and resid 801 through 804' Processing helix chain 'B' and resid 837 through 849 removed outlier: 4.048A pdb=" N SER B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 Processing helix chain 'B' and resid 873 through 892 Processing helix chain 'B' and resid 897 through 902 removed outlier: 3.687A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 919 removed outlier: 3.778A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 955 Processing helix chain 'B' and resid 960 through 990 removed outlier: 4.005A pdb=" N LEU B 965 " --> pdb=" O ILE B 961 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix removed outlier: 4.254A pdb=" N LEU B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 997 through 1013 removed outlier: 4.257A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1032 Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.682A pdb=" N GLY C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 100 through 111 removed outlier: 3.616A pdb=" N LYS C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.800A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 316 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.714A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.978A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 400 Processing helix chain 'C' and resid 402 through 422 removed outlier: 4.260A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.772A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 Processing helix chain 'C' and resid 517 through 536 removed outlier: 3.616A pdb=" N LEU C 535 " --> pdb=" O VAL C 531 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG C 536 " --> pdb=" O GLY C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 558 Processing helix chain 'C' and resid 584 through 600 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 644 through 657 removed outlier: 4.140A pdb=" N GLN C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 707 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 743 through 754 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 783 through 788 removed outlier: 3.582A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 837 through 849 Processing helix chain 'C' and resid 861 through 892 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 905 through 919 removed outlier: 4.040A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 954 removed outlier: 3.568A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 970 Processing helix chain 'C' and resid 973 through 990 removed outlier: 3.873A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 1000 through 1013 removed outlier: 4.056A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 Proline residue: C1023 - end of helix Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 62 through 65 No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.834A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 299 through 316 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.903A pdb=" N VAL A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 386 removed outlier: 3.762A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 403 through 423 removed outlier: 4.671A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 449 removed outlier: 3.702A pdb=" N GLY A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 463 through 495 removed outlier: 3.617A pdb=" N SER A 476 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU A 488 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.994A pdb=" N CYS A 493 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.691A pdb=" N LEU A 544 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 546 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 600 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 692 through 707 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 841 through 847 removed outlier: 3.616A pdb=" N MET A 844 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 847 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 868 removed outlier: 3.656A pdb=" N LEU A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.563A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 3.938A pdb=" N ALA A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 953 removed outlier: 3.515A pdb=" N THR A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 973 through 991 removed outlier: 3.565A pdb=" N VAL A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 997 through 1016 removed outlier: 3.567A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1016 " --> pdb=" O VAL A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 Processing sheet with id= A, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.556A pdb=" N ALA B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN B 81 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 144 Processing sheet with id= C, first strand: chain 'B' and resid 175 through 177 Processing sheet with id= D, first strand: chain 'B' and resid 266 through 268 removed outlier: 9.259A pdb=" N MET B 184 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS B 770 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE B 186 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 772 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET B 188 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET B 774 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.734A pdb=" N SER B 608 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 679 through 683 Processing sheet with id= G, first strand: chain 'B' and resid 724 through 731 Processing sheet with id= H, first strand: chain 'B' and resid 790 through 792 Processing sheet with id= I, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.620A pdb=" N SER C 46 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 322 through 324 removed outlier: 7.111A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C 289 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY C 141 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER C 287 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE C 143 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER C 630 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL C 609 " --> pdb=" O PHE C 628 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE C 628 " --> pdb=" O VAL C 609 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA C 611 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 626 " --> pdb=" O ALA C 611 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 613 " --> pdb=" O THR C 624 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR C 624 " --> pdb=" O ASN C 613 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 574 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.208A pdb=" N TYR C 182 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS C 770 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 217 through 219 removed outlier: 4.160A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 824 through 827 Processing sheet with id= N, first strand: chain 'C' and resid 723 through 731 Processing sheet with id= O, first strand: chain 'C' and resid 790 through 792 Processing sheet with id= P, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.037A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.545A pdb=" N ALA A 47 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.364A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 321 through 324 Processing sheet with id= S, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.650A pdb=" N VAL A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N MET A 184 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS A 770 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE A 186 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR A 772 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N MET A 188 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET A 774 " --> pdb=" O MET A 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 284 through 286 removed outlier: 4.144A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER A 630 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 609 " --> pdb=" O PHE A 628 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 628 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 611 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 626 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN A 613 " --> pdb=" O THR A 624 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR A 624 " --> pdb=" O ASN A 613 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 627 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 717 through 719 removed outlier: 4.318A pdb=" N GLU A 826 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 724 through 731 Processing sheet with id= W, first strand: chain 'A' and resid 790 through 792 Processing sheet with id= X, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.062A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3396 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: 10.18 Time building geometry restraints manager: 10.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3888 1.30 - 1.44: 5859 1.44 - 1.57: 14181 1.57 - 1.70: 30 1.70 - 1.83: 258 Bond restraints: 24216 Sorted by residual: bond pdb=" C ARG B 973 " pdb=" O ARG B 973 " ideal model delta sigma weight residual 1.244 1.185 0.058 1.00e-02 1.00e+04 3.38e+01 bond pdb=" N PRO B 318 " pdb=" CD PRO B 318 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.31e+01 bond pdb=" C GLU C 130 " pdb=" N LYS C 131 " ideal model delta sigma weight residual 1.330 1.393 -0.063 1.32e-02 5.74e+03 2.30e+01 bond pdb=" C GLY C 998 " pdb=" O GLY C 998 " ideal model delta sigma weight residual 1.233 1.286 -0.053 1.13e-02 7.83e+03 2.21e+01 bond pdb=" C ILE A 445 " pdb=" O ILE A 445 " ideal model delta sigma weight residual 1.237 1.176 0.062 1.32e-02 5.74e+03 2.19e+01 ... (remaining 24211 not shown) Histogram of bond angle deviations from ideal: 96.56 - 104.13: 415 104.13 - 111.70: 11010 111.70 - 119.27: 9897 119.27 - 126.84: 11194 126.84 - 134.41: 223 Bond angle restraints: 32739 Sorted by residual: angle pdb=" N GLN B 255 " pdb=" CA GLN B 255 " pdb=" C GLN B 255 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.17e+00 7.31e-01 6.14e+01 angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 111.62 105.50 6.12 7.90e-01 1.60e+00 5.99e+01 angle pdb=" N ILE B 370 " pdb=" CA ILE B 370 " pdb=" C ILE B 370 " ideal model delta sigma weight residual 111.90 105.67 6.23 8.10e-01 1.52e+00 5.91e+01 angle pdb=" N PHE A 563 " pdb=" CA PHE A 563 " pdb=" C PHE A 563 " ideal model delta sigma weight residual 113.41 104.19 9.22 1.22e+00 6.72e-01 5.71e+01 angle pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 120.83 125.26 -4.43 5.90e-01 2.87e+00 5.64e+01 ... (remaining 32734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 14120 35.13 - 70.27: 352 70.27 - 105.40: 22 105.40 - 140.54: 6 140.54 - 175.67: 7 Dihedral angle restraints: 14507 sinusoidal: 5749 harmonic: 8758 Sorted by residual: dihedral pdb=" C ASP B 153 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " ideal model delta harmonic sigma weight residual -122.60 -135.50 12.90 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" C GLU B 414 " pdb=" N GLU B 414 " pdb=" CA GLU B 414 " pdb=" CB GLU B 414 " ideal model delta harmonic sigma weight residual -122.60 -135.05 12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" C THR B 489 " pdb=" N THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta harmonic sigma weight residual -122.00 -133.90 11.90 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 14504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3333 0.114 - 0.228: 419 0.228 - 0.342: 60 0.342 - 0.456: 10 0.456 - 0.571: 2 Chirality restraints: 3824 Sorted by residual: chirality pdb=" CB VAL A 905 " pdb=" CA VAL A 905 " pdb=" CG1 VAL A 905 " pdb=" CG2 VAL A 905 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" C6 PTY A1103 " pdb=" C1 PTY A1103 " pdb=" C5 PTY A1103 " pdb=" O7 PTY A1103 " both_signs ideal model delta sigma weight residual False 2.49 2.01 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" C6 PTY A1109 " pdb=" C1 PTY A1109 " pdb=" C5 PTY A1109 " pdb=" O7 PTY A1109 " both_signs ideal model delta sigma weight residual False 2.49 2.05 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 3821 not shown) Planarity restraints: 4127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 412 " -0.028 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C VAL C 412 " 0.097 2.00e-02 2.50e+03 pdb=" O VAL C 412 " -0.037 2.00e-02 2.50e+03 pdb=" N VAL C 413 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 443 " 0.025 2.00e-02 2.50e+03 5.40e-02 2.91e+01 pdb=" C VAL A 443 " -0.093 2.00e-02 2.50e+03 pdb=" O VAL A 443 " 0.036 2.00e-02 2.50e+03 pdb=" N GLY A 444 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 403 " 0.022 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C GLY A 403 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY A 403 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU A 404 " 0.027 2.00e-02 2.50e+03 ... (remaining 4124 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 420 2.66 - 3.22: 23338 3.22 - 3.78: 37345 3.78 - 4.34: 53727 4.34 - 4.90: 87600 Nonbonded interactions: 202430 Sorted by model distance: nonbonded pdb=" O ASN C 81 " pdb=" OD1 ASN C 81 " model vdw 2.102 3.040 nonbonded pdb=" O VAL A 345 " pdb=" CG2 ILE A 348 " model vdw 2.205 3.460 nonbonded pdb=" OG SER A 836 " pdb=" OE2 GLU A 839 " model vdw 2.212 2.440 nonbonded pdb=" OD1 ASP A 858 " pdb=" N TRP A 859 " model vdw 2.218 2.520 nonbonded pdb=" OD1 ASN A 415 " pdb=" OG SER A 434 " model vdw 2.242 2.440 ... (remaining 202425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 163 or (resid 164 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 385 or (resid 386 an \ d (name N or name CA or name C or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 387 through 478 or (resid 479 and (n \ ame N or name CA or name C or name CB )) or resid 480 through 500 or resid 516 t \ hrough 1033 or (resid 1102 and (name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37)) or (resid 1103 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18)) or (resid 1104 and (na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 \ or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 \ )) or (resid 1105 and (name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)))) selection = (chain 'B' and (resid 1 through 432 or (resid 433 and (name N or name CA or name \ C or name O or name CB )) or resid 434 through 449 or (resid 450 and (name N or \ name CA or name C or name CB or name OG )) or resid 451 through 500 or resid 51 \ 6 through 517 or (resid 518 and (name N or name CA or name C or name O or name C \ B )) or resid 519 through 524 or (resid 525 and (name N or name CA or name C or \ name O or name CB )) or resid 526 through 528 or (resid 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 or (resid 531 and (name N or n \ ame CA or name C or name O or name CB )) or resid 532 through 533 or (resid 534 \ and (name N or name CA or name C or name O or name CB )) or resid 535 or (resid \ 536 and (name N or name CA or name C or name O or name CB )) or resid 537 or (re \ sid 538 and (name N or name CA or name C or name O or name CB )) or resid 539 or \ (resid 540 and (name N or name CA or name C or name O or name CB )) or resid 54 \ 1 through 619 or (resid 620 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name NE or name CZ )) or resid 621 through 846 or (re \ sid 847 through 848 and (name N or name CA or name C or name O or name CB )) or \ resid 849 through 954 or (resid 955 through 956 and (name N or name CA or name C \ or name O or name CB )) or resid 957 through 964 or (resid 965 and (name N or n \ ame CA or name C or name O or name CB )) or resid 966 through 968 or (resid 969 \ and (name N or name CA or name C or name O or name CB )) or resid 970 through 10 \ 25 or (resid 1026 through 1027 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1028 through 1030 or (resid 1031 through 1033 and (name N or na \ me CA or name C or name O or name CB )) or resid 1105 or (resid 1106 and (name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18)) or \ resid 1107 through 1108)) selection = (chain 'C' and (resid 1 through 163 or (resid 164 through 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 385 or (resid 386 an \ d (name N or name CA or name C or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 387 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 449 or ( \ resid 450 and (name N or name CA or name C or name CB or name OG )) or resid 451 \ through 478 or (resid 479 and (name N or name CA or name C or name CB )) or res \ id 480 through 500 or resid 516 through 521 or (resid 522 and (name N or name CA \ or name C or name O or name CB )) or resid 523 through 524 or (resid 525 and (n \ ame N or name CA or name C or name O or name CB )) or resid 526 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ or (resid 531 and (name N or name CA or name C or name O or name CB )) or resid \ 532 through 533 or (resid 534 and (name N or name CA or name C or name O or name \ CB )) or resid 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 or (resid 538 and (name N or name CA or name C or name O \ or name CB )) or resid 539 or (resid 540 and (name N or name CA or name C or na \ me O or name CB )) or resid 541 through 619 or (resid 620 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ )) o \ r resid 621 through 846 or (resid 847 through 848 and (name N or name CA or name \ C or name O or name CB )) or resid 849 through 954 or (resid 955 through 956 an \ d (name N or name CA or name C or name O or name CB )) or resid 957 through 964 \ or (resid 965 and (name N or name CA or name C or name O or name CB )) or resid \ 966 through 968 or (resid 969 and (name N or name CA or name C or name O or name \ CB )) or resid 970 through 1025 or (resid 1026 through 1027 and (name N or name \ CA or name C or name O or name CB )) or resid 1028 through 1030 or (resid 1031 \ through 1033 and (name N or name CA or name C or name O or name CB )) or (resid \ 1104 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 o \ r name C37)) or (resid 1105 and (name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18)) or (resid 1106 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O1 \ 3 or name O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1107 and \ (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name N \ 1 )))) } 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: 2.150 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: 0.030 Extract box with map and model: 11.040 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 65.320 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 0.069 24216 Z= 0.543 Angle : 1.211 10.402 32739 Z= 0.858 Chirality : 0.078 0.571 3824 Planarity : 0.006 0.056 4127 Dihedral : 15.643 175.670 8887 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.44 % Allowed : 2.99 % Favored : 96.56 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 2.22 % 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: -1.19 (0.15), residues: 3051 helix: -0.05 (0.13), residues: 1597 sheet: -1.68 (0.25), residues: 408 loop : -1.36 (0.19), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 427 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 435 average time/residue: 0.3356 time to fit residues: 235.2022 Evaluate side-chains 287 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4333 time to fit residues: 4.4472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 276 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN B 231 ASN C 928 GLN A 577 GLN A 584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24216 Z= 0.205 Angle : 0.547 9.395 32739 Z= 0.284 Chirality : 0.042 0.167 3824 Planarity : 0.004 0.054 4127 Dihedral : 13.224 179.469 3627 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 1.29 % Allowed : 8.86 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.16), residues: 3051 helix: 0.91 (0.13), residues: 1616 sheet: -1.49 (0.25), residues: 401 loop : -0.83 (0.20), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 314 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 32 outliers final: 21 residues processed: 332 average time/residue: 0.3099 time to fit residues: 170.7649 Evaluate side-chains 298 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 277 time to evaluate : 2.564 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2287 time to fit residues: 12.1916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 277 optimal weight: 0.4980 chunk 299 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 275 optimal weight: 3.9990 chunk 94 optimal weight: 0.0770 chunk 222 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 298 ASN C 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A1000 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24216 Z= 0.212 Angle : 0.509 9.336 32739 Z= 0.260 Chirality : 0.041 0.161 3824 Planarity : 0.004 0.048 4127 Dihedral : 11.779 173.471 3627 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.73 % Allowed : 11.12 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.34 (0.16), residues: 3051 helix: 1.22 (0.13), residues: 1626 sheet: -1.26 (0.26), residues: 408 loop : -0.61 (0.20), residues: 1017 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 310 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 7 residues processed: 317 average time/residue: 0.3101 time to fit residues: 163.7824 Evaluate side-chains 292 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 285 time to evaluate : 2.765 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2201 time to fit residues: 6.4394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1001 ASN C 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24216 Z= 0.198 Angle : 0.491 8.384 32739 Z= 0.249 Chirality : 0.041 0.149 3824 Planarity : 0.003 0.048 4127 Dihedral : 11.158 169.436 3627 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.09 % Allowed : 11.73 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.54 (0.16), residues: 3051 helix: 1.39 (0.13), residues: 1620 sheet: -1.15 (0.25), residues: 409 loop : -0.55 (0.20), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 303 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 11 residues processed: 318 average time/residue: 0.3213 time to fit residues: 170.6351 Evaluate side-chains 303 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 292 time to evaluate : 2.875 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2312 time to fit residues: 8.4367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 219 optimal weight: 0.0970 chunk 121 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 203 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1001 ASN C 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24216 Z= 0.204 Angle : 0.489 7.906 32739 Z= 0.247 Chirality : 0.041 0.157 3824 Planarity : 0.003 0.048 4127 Dihedral : 10.642 165.682 3627 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.85 % Allowed : 13.02 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.64 (0.16), residues: 3051 helix: 1.45 (0.13), residues: 1623 sheet: -1.12 (0.25), residues: 409 loop : -0.45 (0.20), residues: 1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 307 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 8 residues processed: 317 average time/residue: 0.3173 time to fit residues: 166.7294 Evaluate side-chains 297 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 289 time to evaluate : 2.681 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2298 time to fit residues: 7.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 244 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1001 ASN C 74 ASN C 284 GLN A 104 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24216 Z= 0.266 Angle : 0.512 8.748 32739 Z= 0.259 Chirality : 0.042 0.209 3824 Planarity : 0.004 0.048 4127 Dihedral : 10.399 163.235 3627 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.29 % Allowed : 13.51 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.62 (0.16), residues: 3051 helix: 1.44 (0.13), residues: 1616 sheet: -1.18 (0.25), residues: 406 loop : -0.43 (0.20), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 294 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 32 outliers final: 17 residues processed: 308 average time/residue: 0.3224 time to fit residues: 165.8125 Evaluate side-chains 303 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2359 time to fit residues: 10.9734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1001 ASN C 74 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24216 Z= 0.165 Angle : 0.483 8.793 32739 Z= 0.243 Chirality : 0.040 0.208 3824 Planarity : 0.003 0.048 4127 Dihedral : 9.952 159.312 3627 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.44 % Allowed : 14.07 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.75 (0.16), residues: 3051 helix: 1.51 (0.13), residues: 1620 sheet: -1.05 (0.25), residues: 409 loop : -0.35 (0.21), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 300 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 4 residues processed: 305 average time/residue: 0.3237 time to fit residues: 165.4281 Evaluate side-chains 289 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 285 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2090 time to fit residues: 5.0712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24216 Z= 0.199 Angle : 0.495 8.283 32739 Z= 0.248 Chirality : 0.041 0.188 3824 Planarity : 0.003 0.048 4127 Dihedral : 9.657 157.439 3627 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.49 % Allowed : 14.92 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.77 (0.16), residues: 3051 helix: 1.53 (0.13), residues: 1618 sheet: -1.04 (0.25), residues: 409 loop : -0.35 (0.21), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 291 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 7 residues processed: 298 average time/residue: 0.3134 time to fit residues: 156.0854 Evaluate side-chains 286 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 279 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2285 time to fit residues: 6.6773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24216 Z= 0.195 Angle : 0.492 8.091 32739 Z= 0.246 Chirality : 0.041 0.189 3824 Planarity : 0.003 0.048 4127 Dihedral : 9.338 150.065 3627 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.16 % Allowed : 15.08 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.81 (0.16), residues: 3051 helix: 1.56 (0.13), residues: 1611 sheet: -1.05 (0.25), residues: 406 loop : -0.30 (0.21), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 450 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 4 residues processed: 293 average time/residue: 0.3435 time to fit residues: 168.9172 Evaluate side-chains 288 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 284 time to evaluate : 2.640 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2527 time to fit residues: 5.5783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 60.851 > 50: distance: 50 - 79: 21.778 distance: 54 - 58: 30.781 distance: 55 - 88: 18.222 distance: 58 - 59: 8.499 distance: 59 - 60: 33.509 distance: 59 - 62: 17.903 distance: 60 - 61: 10.747 distance: 60 - 70: 12.202 distance: 62 - 63: 20.918 distance: 63 - 64: 25.845 distance: 63 - 65: 20.587 distance: 64 - 66: 20.578 distance: 65 - 67: 7.543 distance: 66 - 68: 10.785 distance: 67 - 68: 6.766 distance: 68 - 69: 18.783 distance: 70 - 71: 21.061 distance: 71 - 72: 32.340 distance: 71 - 74: 17.967 distance: 72 - 73: 7.678 distance: 72 - 79: 44.536 distance: 74 - 75: 25.739 distance: 75 - 76: 12.539 distance: 76 - 77: 7.695 distance: 76 - 78: 27.278 distance: 79 - 80: 29.618 distance: 80 - 81: 7.715 distance: 80 - 83: 29.380 distance: 81 - 82: 35.015 distance: 81 - 88: 8.069 distance: 83 - 84: 33.051 distance: 84 - 85: 44.438 distance: 85 - 86: 30.308 distance: 85 - 87: 36.079 distance: 88 - 89: 13.177 distance: 89 - 90: 26.234 distance: 89 - 92: 29.955 distance: 90 - 91: 34.209 distance: 90 - 99: 19.018 distance: 92 - 93: 11.993 distance: 93 - 94: 24.556 distance: 94 - 95: 38.572 distance: 95 - 96: 25.088 distance: 96 - 97: 30.675 distance: 96 - 98: 16.840 distance: 99 - 100: 21.595 distance: 100 - 101: 50.070 distance: 100 - 103: 37.993 distance: 101 - 102: 10.328 distance: 101 - 107: 35.706 distance: 103 - 104: 37.958 distance: 104 - 105: 39.876 distance: 104 - 106: 49.801 distance: 108 - 109: 32.766 distance: 108 - 111: 8.402 distance: 109 - 110: 25.361 distance: 109 - 113: 8.913 distance: 111 - 112: 38.205 distance: 113 - 114: 13.818 distance: 114 - 115: 10.923 distance: 115 - 116: 34.366 distance: 115 - 117: 12.094 distance: 117 - 118: 14.058 distance: 118 - 119: 25.275 distance: 118 - 121: 17.957 distance: 119 - 120: 16.898 distance: 119 - 125: 35.345 distance: 121 - 122: 22.689 distance: 122 - 123: 18.327 distance: 122 - 124: 6.981 distance: 125 - 126: 15.225 distance: 126 - 127: 17.252 distance: 126 - 129: 4.940 distance: 127 - 128: 24.531 distance: 127 - 134: 23.812 distance: 129 - 130: 28.053 distance: 130 - 131: 27.019 distance: 131 - 132: 26.148 distance: 131 - 133: 16.615 distance: 134 - 135: 15.188 distance: 135 - 136: 19.084 distance: 135 - 138: 32.567 distance: 136 - 137: 13.786 distance: 136 - 139: 19.109 distance: 137 - 159: 25.700