Starting phenix.real_space_refine on Sun May 25 00:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cc3_45433/05_2025/9cc3_45433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cc3_45433/05_2025/9cc3_45433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cc3_45433/05_2025/9cc3_45433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cc3_45433/05_2025/9cc3_45433.map" model { file = "/net/cci-nas-00/data/ceres_data/9cc3_45433/05_2025/9cc3_45433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cc3_45433/05_2025/9cc3_45433.cif" } resolution = 3.23 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= 0.001 sd= 0.074 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 16312 2.51 5 N 4426 2.21 5 O 4910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25779 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 151 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4303 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 25, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4202 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 25, 'TRANS': 518} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4322 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 4184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4184 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 25, 'TRANS': 517} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4319 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 25, 'TRANS': 539} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "F" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4186 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.90, per 1000 atoms: 0.58 Number of scatterers: 25779 At special positions: 0 Unit cell: (136.664, 134.061, 161.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 8 15.00 Mg 4 11.99 O 4910 8.00 N 4426 7.00 C 16312 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: 5.78 Conformation dependent library (CDL) restraints added in 3.1 seconds 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6254 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 35 sheets defined 54.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'G' and resid -1 through 1 No H-bonds generated for 'chain 'G' and resid -1 through 1' Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.928A pdb=" N UNK G 6 " --> pdb=" O UNK G 2 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N UNK G 13 " --> pdb=" O UNK G 9 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N UNK G 14 " --> pdb=" O UNK G 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 408 removed outlier: 3.819A pdb=" N ARG A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.896A pdb=" N ARG A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.559A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.663A pdb=" N ILE A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.726A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 615 through 618 removed outlier: 3.596A pdb=" N ASN A 618 " --> pdb=" O GLN A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 629 through 633 removed outlier: 4.254A pdb=" N LYS A 632 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 4.039A pdb=" N ASP A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 704 removed outlier: 3.522A pdb=" N CYS A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 833 through 838 removed outlier: 3.583A pdb=" N THR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.993A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.836A pdb=" N LYS B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.802A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.693A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 531 through 541 removed outlier: 3.888A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.888A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.716A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 641 through 645 removed outlier: 4.043A pdb=" N THR B 644 " --> pdb=" O VAL B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.520A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.531A pdb=" N GLN B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.568A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.936A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 408 removed outlier: 3.838A pdb=" N GLU C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.927A pdb=" N GLU C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.847A pdb=" N GLU C 427 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 452 through 466 Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.787A pdb=" N ARG C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 541 removed outlier: 3.968A pdb=" N ALA C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.637A pdb=" N ILE C 595 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 608 removed outlier: 3.662A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.616A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 removed outlier: 3.507A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 924 through 929 removed outlier: 3.553A pdb=" N THR C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.910A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C 944 " --> pdb=" O ARG C 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 408 removed outlier: 3.563A pdb=" N GLY D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 426 removed outlier: 4.441A pdb=" N GLU D 419 " --> pdb=" O ASP D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.631A pdb=" N ASP D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 467 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 528 through 541 removed outlier: 3.754A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 592 through 595 removed outlier: 3.514A pdb=" N ILE D 595 " --> pdb=" O VAL D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 602 through 602 No H-bonds generated for 'chain 'D' and resid 602 through 602' Processing helix chain 'D' and resid 603 through 611 removed outlier: 4.266A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 741 through 745 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 removed outlier: 3.670A pdb=" N LYS D 898 " --> pdb=" O GLY D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 924 through 929 removed outlier: 3.511A pdb=" N THR D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.788A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 408 removed outlier: 3.674A pdb=" N ARG E 381 " --> pdb=" O GLN E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 413 through 424 removed outlier: 4.082A pdb=" N ILE E 417 " --> pdb=" O ASP E 413 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU E 418 " --> pdb=" O LYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 removed outlier: 4.257A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 490 removed outlier: 3.676A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 512 Processing helix chain 'E' and resid 528 through 541 removed outlier: 3.591A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 572 through 581 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.828A pdb=" N ILE E 595 " --> pdb=" O VAL E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 612 removed outlier: 4.004A pdb=" N LEU E 607 " --> pdb=" O PRO E 603 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 618 Processing helix chain 'E' and resid 646 through 651 removed outlier: 3.530A pdb=" N ASP E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 692 through 703 removed outlier: 3.605A pdb=" N LEU E 696 " --> pdb=" O SER E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 738 through 745 removed outlier: 3.656A pdb=" N LEU E 742 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.598A pdb=" N GLN E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 838 Processing helix chain 'E' and resid 853 through 855 No H-bonds generated for 'chain 'E' and resid 853 through 855' Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 906 Processing helix chain 'E' and resid 916 through 921 removed outlier: 3.620A pdb=" N TYR E 921 " --> pdb=" O LYS E 917 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 929 removed outlier: 3.603A pdb=" N THR E 928 " --> pdb=" O ALA E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.947A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 409 removed outlier: 3.973A pdb=" N LYS F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 425 removed outlier: 4.031A pdb=" N LEU F 425 " --> pdb=" O PHE F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 445 removed outlier: 4.952A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU F 440 " --> pdb=" O ASP F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'F' and resid 452 through 466 Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 528 through 540 removed outlier: 4.166A pdb=" N ILE F 532 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 603 through 612 removed outlier: 3.559A pdb=" N LEU F 607 " --> pdb=" O PRO F 603 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 4.066A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 652 removed outlier: 3.992A pdb=" N ARG F 650 " --> pdb=" O PRO F 646 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 646 through 652' Processing helix chain 'F' and resid 662 through 683 removed outlier: 3.534A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL F 675 " --> pdb=" O GLU F 671 " (cutoff:3.500A) Proline residue: F 676 - end of helix Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 741 through 746 removed outlier: 4.124A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 833 through 838 Processing helix chain 'F' and resid 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.772A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.886A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP F 944 " --> pdb=" O ARG F 940 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 3.627A pdb=" N ASP A 590 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 519 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA A 639 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE A 521 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 654 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 520 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 620 Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA4, first strand: chain 'A' and resid 764 through 769 removed outlier: 6.190A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.735A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 910 " --> pdb=" O HIS A 934 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 936 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.565A pdb=" N GLU A 882 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 544 through 548 removed outlier: 3.649A pdb=" N ASP B 590 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 654 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 689 through 690 removed outlier: 3.594A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 764 through 770 removed outlier: 6.146A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.931A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB3, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.905A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB5, first strand: chain 'C' and resid 689 through 690 removed outlier: 4.016A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 765 through 769 removed outlier: 6.102A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 877 through 879 removed outlier: 7.063A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB9, first strand: chain 'D' and resid 544 through 548 removed outlier: 4.182A pdb=" N ASP D 590 " --> pdb=" O PHE D 547 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 689 through 690 removed outlier: 3.694A pdb=" N LYS D 690 " --> pdb=" O VAL D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 764 through 771 removed outlier: 5.975A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 877 through 879 removed outlier: 3.690A pdb=" N ILE D 910 " --> pdb=" O GLU D 932 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC5, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.996A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 619 through 620 Processing sheet with id=AC7, first strand: chain 'E' and resid 689 through 691 Processing sheet with id=AC8, first strand: chain 'E' and resid 765 through 771 removed outlier: 5.933A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.907A pdb=" N ALA E 878 " --> pdb=" O VAL E 911 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AD2, first strand: chain 'F' and resid 544 through 548 removed outlier: 4.370A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 619 through 620 Processing sheet with id=AD4, first strand: chain 'F' and resid 689 through 691 Processing sheet with id=AD5, first strand: chain 'F' and resid 764 through 766 removed outlier: 6.126A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 769 through 771 Processing sheet with id=AD7, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.953A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 910 " --> pdb=" O GLU F 932 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 882 through 883 removed outlier: 3.553A pdb=" N GLU F 882 " --> pdb=" O LEU F 890 " (cutoff:3.500A) 1252 hydrogen bonds defined for protein. 3648 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: 8.55 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8592 1.34 - 1.46: 5024 1.46 - 1.58: 12399 1.58 - 1.69: 12 1.69 - 1.81: 196 Bond restraints: 26223 Sorted by residual: bond pdb=" C ASN E 584 " pdb=" N PRO E 585 " ideal model delta sigma weight residual 1.328 1.354 -0.026 1.26e-02 6.30e+03 4.31e+00 bond pdb=" CA VAL F 429 " pdb=" CB VAL F 429 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.31e-02 5.83e+03 2.44e+00 bond pdb=" CA VAL A 429 " pdb=" CB VAL A 429 " ideal model delta sigma weight residual 1.527 1.545 -0.019 1.31e-02 5.83e+03 2.03e+00 bond pdb=" CA VAL A 658 " pdb=" CB VAL A 658 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.72e+00 bond pdb=" CA LEU E 425 " pdb=" C LEU E 425 " ideal model delta sigma weight residual 1.519 1.533 -0.014 1.32e-02 5.74e+03 1.13e+00 ... (remaining 26218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 34947 1.72 - 3.44: 480 3.44 - 5.15: 81 5.15 - 6.87: 29 6.87 - 8.59: 1 Bond angle restraints: 35538 Sorted by residual: angle pdb=" N VAL D 434 " pdb=" CA VAL D 434 " pdb=" C VAL D 434 " ideal model delta sigma weight residual 113.53 108.90 4.63 9.80e-01 1.04e+00 2.23e+01 angle pdb=" N VAL B 549 " pdb=" CA VAL B 549 " pdb=" C VAL B 549 " ideal model delta sigma weight residual 111.91 109.21 2.70 8.90e-01 1.26e+00 9.22e+00 angle pdb=" N VAL A 430 " pdb=" CA VAL A 430 " pdb=" C VAL A 430 " ideal model delta sigma weight residual 108.63 111.12 -2.49 8.60e-01 1.35e+00 8.36e+00 angle pdb=" C GLU F 583 " pdb=" N ASN F 584 " pdb=" CA ASN F 584 " ideal model delta sigma weight residual 122.89 119.81 3.08 1.12e+00 7.97e-01 7.58e+00 angle pdb=" CA VAL F 626 " pdb=" C VAL F 626 " pdb=" N PRO F 627 " ideal model delta sigma weight residual 116.57 119.17 -2.60 9.80e-01 1.04e+00 7.02e+00 ... (remaining 35533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.70: 14849 18.70 - 37.39: 944 37.39 - 56.09: 137 56.09 - 74.79: 29 74.79 - 93.48: 24 Dihedral angle restraints: 15983 sinusoidal: 6296 harmonic: 9687 Sorted by residual: dihedral pdb=" CA ARG E 424 " pdb=" C ARG E 424 " pdb=" N LEU E 425 " pdb=" CA LEU E 425 " ideal model delta harmonic sigma weight residual 180.00 -152.65 -27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" C5' ADP D1001 " pdb=" O5' ADP D1001 " pdb=" PA ADP D1001 " pdb=" O2A ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 -153.48 93.48 1 2.00e+01 2.50e-03 2.55e+01 dihedral pdb=" CA ARG D 874 " pdb=" C ARG D 874 " pdb=" N GLN D 875 " pdb=" CA GLN D 875 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 15980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2564 0.030 - 0.059: 995 0.059 - 0.089: 361 0.089 - 0.118: 176 0.118 - 0.148: 22 Chirality restraints: 4118 Sorted by residual: chirality pdb=" CA ILE D 645 " pdb=" N ILE D 645 " pdb=" C ILE D 645 " pdb=" CB ILE D 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE E 645 " pdb=" N ILE E 645 " pdb=" C ILE E 645 " pdb=" CB ILE E 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE B 645 " pdb=" N ILE B 645 " pdb=" C ILE B 645 " pdb=" CB ILE B 645 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 4115 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 738 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E 739 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 739 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 739 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 761 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 762 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 762 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 762 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 738 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO F 739 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 739 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 739 " 0.023 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 228 2.63 - 3.20: 23583 3.20 - 3.77: 39598 3.77 - 4.33: 54110 4.33 - 4.90: 89486 Nonbonded interactions: 207005 Sorted by model distance: nonbonded pdb=" O3B ADP E1001 " pdb="MG MG E1002 " model vdw 2.068 2.170 nonbonded pdb=" O2A ADP E1001 " pdb="MG MG E1002 " model vdw 2.087 2.170 nonbonded pdb=" O2B ADP B1001 " pdb="MG MG B1002 " model vdw 2.120 2.170 nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1002 " model vdw 2.124 2.170 nonbonded pdb=" O2B ADP C1001 " pdb="MG MG C1002 " model vdw 2.188 2.170 ... (remaining 207000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 448 or (res \ id 449 and (name N or name CA or name C or name O or name CB )) or resid 450 thr \ ough 595 or resid 603 through 631 or (resid 632 and (name N or name CA or name C \ or name O or name CB )) or resid 633 through 685 or (resid 686 and (name N or n \ ame CA or name C or name O or name CB )) or resid 687 through 689 or (resid 690 \ and (name N or name CA or name C or name O or name CB )) or resid 691 through 77 \ 2 or (resid 773 and (name N or name CA or name C or name O or name CB )) or resi \ d 774 through 788 or resid 796 through 836 or (resid 837 and (name N or name CA \ or name C or name O or name CB )) or resid 838 through 948 or (resid 949 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 595 or resi \ d 603 through 631 or (resid 632 and (name N or name CA or name C or name O or na \ me CB )) or resid 633 through 685 or (resid 686 and (name N or name CA or name C \ or name O or name CB )) or resid 687 through 689 or (resid 690 and (name N or n \ ame CA or name C or name O or name CB )) or resid 691 through 772 or (resid 773 \ and (name N or name CA or name C or name O or name CB )) or resid 774 through 83 \ 6 or (resid 837 and (name N or name CA or name C or name O or name CB )) or resi \ d 838 through 948 or (resid 949 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'C' and (resid 396 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 448 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throug \ h 595 or resid 603 through 631 or (resid 632 and (name N or name CA or name C or \ name O or name CB )) or resid 633 through 685 or (resid 686 and (name N or name \ CA or name C or name O or name CB )) or resid 687 through 689 or (resid 690 and \ (name N or name CA or name C or name O or name CB )) or resid 691 through 772 o \ r (resid 773 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 74 through 788 or resid 790 or resid 797 through 836 or (resid 837 and (name N o \ r name CA or name C or name O or name CB )) or resid 838 through 948 or (resid 9 \ 49 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 595 or resi \ d 603 through 631 or (resid 632 and (name N or name CA or name C or name O or na \ me CB )) or resid 633 through 685 or (resid 686 and (name N or name CA or name C \ or name O or name CB )) or resid 687 through 788 or resid 796 through 948 or (r \ esid 949 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 413 or (resid 414 and (name N or name CA or \ name C or name O or name CB )) or resid 415 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 595 or resi \ d 603 through 631 or (resid 632 and (name N or name CA or name C or name O or na \ me CB )) or resid 633 through 689 or (resid 690 and (name N or name CA or name C \ or name O or name CB )) or resid 691 through 772 or (resid 773 and (name N or n \ ame CA or name C or name O or name CB )) or resid 774 through 788 or resid 796 t \ hrough 836 or (resid 837 and (name N or name CA or name C or name O or name CB ) \ ) or resid 838 through 949)) selection = (chain 'F' and ((resid 396 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 through 410 or (resid 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 595 or resi \ d 603 through 685 or (resid 686 and (name N or name CA or name C or name O or na \ me CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C \ or name O or name CB )) or resid 691 through 772 or (resid 773 and (name N or n \ ame CA or name C or name O or name CB )) or resid 774 through 788 or resid 796 t \ hrough 836 or (resid 837 and (name N or name CA or name C or name O or name CB ) \ ) or resid 838 through 948 or (resid 949 and (name N or name CA or name C or nam \ e O or name CB )))) } 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: 0.950 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: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 52.940 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.090 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26223 Z= 0.113 Angle : 0.552 8.589 35538 Z= 0.301 Chirality : 0.040 0.148 4118 Planarity : 0.004 0.045 4578 Dihedral : 12.884 93.482 9729 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.22 (0.15), residues: 3287 helix: 1.56 (0.14), residues: 1476 sheet: 0.52 (0.25), residues: 438 loop : 0.20 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 464 HIS 0.003 0.001 HIS D 938 PHE 0.010 0.001 PHE E 547 TYR 0.010 0.001 TYR A 939 ARG 0.009 0.000 ARG E 422 Details of bonding type rmsd hydrogen bonds : bond 0.16668 ( 1252) hydrogen bonds : angle 6.55918 ( 3648) covalent geometry : bond 0.00209 (26223) covalent geometry : angle 0.55228 (35538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 3.017 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8946 (tpp) cc_final: 0.8136 (tpp) REVERT: A 439 ASP cc_start: 0.8870 (m-30) cc_final: 0.8229 (m-30) REVERT: D 756 MET cc_start: 0.8878 (ttm) cc_final: 0.8525 (ttp) REVERT: E 420 LYS cc_start: 0.8548 (tmtt) cc_final: 0.7685 (tmtt) REVERT: E 574 ILE cc_start: 0.8516 (mm) cc_final: 0.8282 (mm) REVERT: E 766 MET cc_start: 0.8499 (ttt) cc_final: 0.8219 (ttp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3396 time to fit residues: 129.7803 Evaluate side-chains 168 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.111773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.085264 restraints weight = 45818.200| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.58 r_work: 0.3092 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26223 Z= 0.184 Angle : 0.580 9.542 35538 Z= 0.292 Chirality : 0.043 0.164 4118 Planarity : 0.004 0.044 4578 Dihedral : 5.136 106.120 3647 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.52 % Allowed : 4.64 % Favored : 94.84 % 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: 1.22 (0.15), residues: 3287 helix: 1.55 (0.13), residues: 1516 sheet: 0.53 (0.25), residues: 430 loop : 0.17 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 770 HIS 0.009 0.001 HIS C 451 PHE 0.013 0.002 PHE D 547 TYR 0.015 0.002 TYR A 757 ARG 0.005 0.000 ARG E 424 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1252) hydrogen bonds : angle 4.94896 ( 3648) covalent geometry : bond 0.00443 (26223) covalent geometry : angle 0.58028 (35538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 3.019 Fit side-chains REVERT: A 435 MET cc_start: 0.8933 (tpp) cc_final: 0.8731 (tpp) REVERT: B 427 GLU cc_start: 0.8013 (pm20) cc_final: 0.7759 (pm20) REVERT: C 700 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8465 (mp) REVERT: D 489 GLU cc_start: 0.8475 (tt0) cc_final: 0.8240 (tm-30) REVERT: D 653 MET cc_start: 0.8686 (mtm) cc_final: 0.8197 (mtp) REVERT: D 756 MET cc_start: 0.8915 (ttm) cc_final: 0.8512 (ttp) REVERT: E 420 LYS cc_start: 0.8562 (tmtt) cc_final: 0.8247 (tptp) REVERT: E 432 LYS cc_start: 0.8780 (tppt) cc_final: 0.8414 (tppt) REVERT: E 574 ILE cc_start: 0.8675 (mm) cc_final: 0.8447 (mm) REVERT: E 766 MET cc_start: 0.8643 (ttt) cc_final: 0.8441 (ttt) REVERT: E 869 MET cc_start: 0.8780 (mtm) cc_final: 0.8573 (mtp) outliers start: 14 outliers final: 10 residues processed: 196 average time/residue: 0.3440 time to fit residues: 113.2123 Evaluate side-chains 179 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain F residue 620 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 179 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 274 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 155 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 616 ASN ** E 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.112401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086094 restraints weight = 45196.914| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.56 r_work: 0.3128 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26223 Z= 0.104 Angle : 0.514 10.163 35538 Z= 0.255 Chirality : 0.040 0.189 4118 Planarity : 0.004 0.044 4578 Dihedral : 4.974 102.632 3647 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.77 % Allowed : 6.30 % Favored : 92.92 % 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: 1.36 (0.15), residues: 3287 helix: 1.71 (0.13), residues: 1525 sheet: 0.49 (0.25), residues: 432 loop : 0.22 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 464 HIS 0.004 0.001 HIS E 451 PHE 0.011 0.001 PHE E 820 TYR 0.011 0.001 TYR B 939 ARG 0.005 0.000 ARG C 482 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1252) hydrogen bonds : angle 4.59706 ( 3648) covalent geometry : bond 0.00230 (26223) covalent geometry : angle 0.51429 (35538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 2.716 Fit side-chains revert: symmetry clash REVERT: B 427 GLU cc_start: 0.8020 (pm20) cc_final: 0.7667 (pm20) REVERT: C 653 MET cc_start: 0.8540 (mtm) cc_final: 0.8252 (mtm) REVERT: C 700 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8444 (mp) REVERT: D 489 GLU cc_start: 0.8694 (tt0) cc_final: 0.8468 (tm-30) REVERT: D 653 MET cc_start: 0.8526 (mtm) cc_final: 0.8155 (mtp) REVERT: D 756 MET cc_start: 0.8895 (ttm) cc_final: 0.8497 (ttm) REVERT: E 574 ILE cc_start: 0.8619 (mm) cc_final: 0.8401 (mm) REVERT: E 766 MET cc_start: 0.8543 (ttt) cc_final: 0.8270 (ttt) REVERT: E 869 MET cc_start: 0.8706 (mtm) cc_final: 0.8489 (mtp) outliers start: 21 outliers final: 15 residues processed: 205 average time/residue: 0.3439 time to fit residues: 115.6750 Evaluate side-chains 181 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 620 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 107 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 291 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 GLN E 788 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.112546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086306 restraints weight = 45427.121| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.55 r_work: 0.3130 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26223 Z= 0.099 Angle : 0.505 10.636 35538 Z= 0.248 Chirality : 0.040 0.153 4118 Planarity : 0.004 0.045 4578 Dihedral : 4.880 100.622 3647 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.11 % Allowed : 7.11 % Favored : 91.78 % 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: 1.44 (0.15), residues: 3287 helix: 1.82 (0.13), residues: 1530 sheet: 0.52 (0.25), residues: 432 loop : 0.20 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 770 HIS 0.003 0.001 HIS E 451 PHE 0.010 0.001 PHE E 820 TYR 0.012 0.001 TYR B 939 ARG 0.007 0.000 ARG F 786 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 1252) hydrogen bonds : angle 4.40004 ( 3648) covalent geometry : bond 0.00224 (26223) covalent geometry : angle 0.50491 (35538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 2.990 Fit side-chains REVERT: B 427 GLU cc_start: 0.8020 (pm20) cc_final: 0.7609 (pm20) REVERT: C 700 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8432 (mp) REVERT: C 709 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7255 (p) REVERT: D 489 GLU cc_start: 0.8780 (tt0) cc_final: 0.8566 (tm-30) REVERT: D 649 LEU cc_start: 0.8582 (mt) cc_final: 0.8291 (mt) REVERT: D 653 MET cc_start: 0.8536 (mtm) cc_final: 0.8250 (mtp) REVERT: D 756 MET cc_start: 0.8897 (ttm) cc_final: 0.8455 (ttm) REVERT: E 574 ILE cc_start: 0.8613 (mm) cc_final: 0.8398 (mm) REVERT: E 766 MET cc_start: 0.8668 (ttt) cc_final: 0.8447 (ttt) outliers start: 30 outliers final: 19 residues processed: 212 average time/residue: 0.3287 time to fit residues: 116.6522 Evaluate side-chains 187 residues out of total 2851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 620 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 70.4813 > 50: distance: 96 - 217: 35.014 distance: 99 - 233: 28.839 distance: 112 - 236: 34.182 distance: 115 - 247: 34.872 distance: 179 - 184: 34.187 distance: 184 - 185: 22.483 distance: 185 - 186: 19.011 distance: 185 - 188: 19.352 distance: 186 - 187: 40.510 distance: 186 - 192: 32.974 distance: 187 - 207: 37.443 distance: 188 - 189: 56.904 distance: 189 - 191: 40.012 distance: 192 - 193: 5.601 distance: 193 - 196: 40.040 distance: 194 - 195: 40.537 distance: 194 - 198: 40.369 distance: 196 - 197: 56.658 distance: 199 - 202: 51.785 distance: 200 - 201: 42.298 distance: 202 - 203: 53.001 distance: 203 - 204: 55.439 distance: 204 - 205: 41.249 distance: 205 - 206: 56.919 distance: 208 - 209: 57.441 distance: 208 - 211: 39.320 distance: 209 - 210: 39.285 distance: 209 - 214: 56.678 distance: 211 - 213: 40.115 distance: 215 - 216: 38.683 distance: 215 - 218: 10.300 distance: 216 - 217: 39.269 distance: 216 - 222: 40.115 distance: 218 - 219: 34.215 distance: 219 - 220: 56.436 distance: 219 - 221: 5.521 distance: 222 - 223: 57.585 distance: 223 - 224: 52.235 distance: 223 - 226: 39.948 distance: 224 - 225: 42.093 distance: 224 - 233: 28.069 distance: 226 - 227: 18.804 distance: 227 - 228: 18.682 distance: 227 - 229: 43.614 distance: 228 - 230: 39.820 distance: 229 - 231: 42.708 distance: 230 - 232: 57.279 distance: 231 - 232: 25.754 distance: 233 - 234: 40.201 distance: 234 - 235: 49.267 distance: 234 - 237: 49.219 distance: 235 - 236: 55.683 distance: 235 - 241: 48.406 distance: 237 - 238: 40.115 distance: 237 - 239: 69.764 distance: 238 - 240: 45.362 distance: 241 - 242: 27.091 distance: 242 - 245: 20.415 distance: 243 - 244: 56.341 distance: 245 - 246: 42.531 distance: 248 - 251: 41.540 distance: 249 - 254: 40.121 distance: 251 - 252: 39.689 distance: 251 - 253: 55.444 distance: 254 - 255: 57.386 distance: 255 - 256: 40.161 distance: 256 - 259: 33.871