Starting phenix.real_space_refine (version: dev) on Thu Mar 16 23:49:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/03_2023/7ksl_23019_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/03_2023/7ksl_23019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/03_2023/7ksl_23019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/03_2023/7ksl_23019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/03_2023/7ksl_23019_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksl_23019/03_2023/7ksl_23019_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.045 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 489": "OE1" <-> "OE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 785": "NH1" <-> "NH2" Residue "C ARG 786": "NH1" <-> "NH2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C ARG 871": "NH1" <-> "NH2" Residue "C ARG 874": "NH1" <-> "NH2" Residue "C GLU 897": "OE1" <-> "OE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 652": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ASP 744": "OD1" <-> "OD2" Residue "B ARG 785": "NH1" <-> "NH2" Residue "B ARG 871": "NH1" <-> "NH2" Residue "B ARG 874": "NH1" <-> "NH2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B ASP 919": "OD1" <-> "OD2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F ARG 482": "NH1" <-> "NH2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ASP 590": "OD1" <-> "OD2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "F GLU 647": "OE1" <-> "OE2" Residue "F GLU 671": "OE1" <-> "OE2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 679": "NH1" <-> "NH2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F GLU 736": "OE1" <-> "OE2" Residue "F PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 755": "NH1" <-> "NH2" Residue "F ARG 785": "NH1" <-> "NH2" Residue "F ARG 786": "NH1" <-> "NH2" Residue "F GLU 801": "OE1" <-> "OE2" Residue "F GLU 941": "OE1" <-> "OE2" Residue "E ASP 439": "OD1" <-> "OD2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "E ARG 679": "NH1" <-> "NH2" Residue "E ASP 685": "OD1" <-> "OD2" Residue "E GLU 717": "OE1" <-> "OE2" Residue "E PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 755": "NH1" <-> "NH2" Residue "E ARG 785": "NH1" <-> "NH2" Residue "E ARG 786": "NH1" <-> "NH2" Residue "E ASP 789": "OD1" <-> "OD2" Residue "E PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 18306 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3291 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 335 Chain: "B" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3770 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 177 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3826 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 141 Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3881 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 116 Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3403 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.69, per 1000 atoms: 0.58 Number of scatterers: 18306 At special positions: 0 Unit cell: (117.3, 132.25, 132.25, 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 87 16.00 P 10 15.00 O 3436 8.00 N 3162 7.00 C 11611 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: 6.96 Conformation dependent library (CDL) restraints added in 2.8 seconds 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 24 sheets defined 41.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 453 through 467 Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.611A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 558 through 580 removed outlier: 4.326A pdb=" N ILE C 573 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 575 " --> pdb=" O LYS C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 613 through 616 No H-bonds generated for 'chain 'C' and resid 613 through 616' Processing helix chain 'C' and resid 647 through 650 No H-bonds generated for 'chain 'C' and resid 647 through 650' Processing helix chain 'C' and resid 663 through 672 Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 693 through 702 Processing helix chain 'C' and resid 710 through 728 Processing helix chain 'C' and resid 741 through 745 Processing helix chain 'C' and resid 808 through 828 Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 5.281A pdb=" N GLY C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N CYS C 858 " --> pdb=" O PRO C 854 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR C 859 " --> pdb=" O SER C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 914 through 920 removed outlier: 4.886A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 945 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.879A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 removed outlier: 4.086A pdb=" N ASN B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.541A pdb=" N GLU B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 573 through 580 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 647 through 650 No H-bonds generated for 'chain 'B' and resid 647 through 650' Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 729 Processing helix chain 'B' and resid 743 through 746 No H-bonds generated for 'chain 'B' and resid 743 through 746' Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.545A pdb=" N GLN B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) 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 857 through 869 Processing helix chain 'B' and resid 895 through 905 removed outlier: 3.651A pdb=" N ALA B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 920 removed outlier: 5.005A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 946 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.834A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.511A pdb=" N LYS A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 652 removed outlier: 4.310A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 removed outlier: 4.890A pdb=" N VAL A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 728 Processing helix chain 'A' and resid 808 through 828 removed outlier: 3.755A pdb=" N GLN A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Proline residue: A 854 - end of helix No H-bonds generated for 'chain 'A' and resid 850 through 855' Processing helix chain 'A' and resid 857 through 869 Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 939 through 945 Processing helix chain 'F' and resid 422 through 427 Processing helix chain 'F' and resid 432 through 446 removed outlier: 3.686A pdb=" N ASP F 436 " --> pdb=" O LYS F 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 480 through 490 removed outlier: 3.907A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 510 Processing helix chain 'F' and resid 531 through 540 Processing helix chain 'F' and resid 555 through 559 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 604 through 610 Processing helix chain 'F' and resid 613 through 616 No H-bonds generated for 'chain 'F' and resid 613 through 616' Processing helix chain 'F' and resid 647 through 652 removed outlier: 4.051A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 672 Processing helix chain 'F' and resid 674 through 682 Processing helix chain 'F' and resid 693 through 703 Processing helix chain 'F' and resid 710 through 728 removed outlier: 3.666A pdb=" N LYS F 714 " --> pdb=" O ARG F 710 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL F 719 " --> pdb=" O GLN F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 745 No H-bonds generated for 'chain 'F' and resid 742 through 745' Processing helix chain 'F' and resid 808 through 828 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 857 through 869 Processing helix chain 'F' and resid 895 through 904 Processing helix chain 'F' and resid 917 through 920 No H-bonds generated for 'chain 'F' and resid 917 through 920' Processing helix chain 'F' and resid 939 through 946 Processing helix chain 'E' and resid 422 through 425 No H-bonds generated for 'chain 'E' and resid 422 through 425' Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 453 through 467 Processing helix chain 'E' and resid 480 through 489 removed outlier: 4.227A pdb=" N GLU E 488 " --> pdb=" O GLN E 484 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU E 489 " --> pdb=" O ALA E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 509 Processing helix chain 'E' and resid 529 through 539 removed outlier: 3.559A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 580 Processing helix chain 'E' and resid 603 through 610 Processing helix chain 'E' and resid 647 through 650 No H-bonds generated for 'chain 'E' and resid 647 through 650' Processing helix chain 'E' and resid 663 through 672 Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 710 through 728 Processing helix chain 'E' and resid 808 through 826 Processing helix chain 'E' and resid 850 through 869 Proline residue: E 854 - end of helix removed outlier: 5.791A pdb=" N GLY E 857 " --> pdb=" O GLY E 853 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS E 858 " --> pdb=" O PRO E 854 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR E 859 " --> pdb=" O SER E 855 " (cutoff:3.500A) Processing helix chain 'E' and resid 896 through 905 Processing helix chain 'E' and resid 914 through 921 removed outlier: 3.865A pdb=" N LYS E 917 " --> pdb=" O ALA E 914 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP E 919 " --> pdb=" O ASN E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 928 No H-bonds generated for 'chain 'E' and resid 926 through 928' Processing helix chain 'E' and resid 939 through 946 Processing sheet with id= A, first strand: chain 'C' and resid 636 through 638 removed outlier: 6.196A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU C 654 " --> pdb=" O CYS C 520 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR C 522 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 656 " --> pdb=" O TYR C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 764 through 771 Processing sheet with id= C, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.760A pdb=" N CYS C 909 " --> pdb=" O ALA C 878 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU C 932 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU C 912 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS C 934 " --> pdb=" O LEU C 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 654 through 657 removed outlier: 6.244A pdb=" N PHE B 635 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE B 521 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 764 through 771 removed outlier: 6.360A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 909 through 913 removed outlier: 6.032A pdb=" N GLU B 932 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU B 912 " --> pdb=" O GLU B 932 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS B 934 " --> pdb=" O LEU B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 636 through 639 removed outlier: 6.804A pdb=" N LEU A 519 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ALA A 639 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE A 521 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU A 654 " --> pdb=" O CYS A 520 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR A 522 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 656 " --> pdb=" O TYR A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 545 through 548 Processing sheet with id= I, first strand: chain 'A' and resid 689 through 691 removed outlier: 7.116A pdb=" N VAL A 735 " --> pdb=" O LYS A 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 764 through 767 removed outlier: 6.398A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.667A pdb=" N CYS A 909 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A 932 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 912 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS A 934 " --> pdb=" O LEU A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 636 through 639 removed outlier: 6.786A pdb=" N LEU F 519 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ALA F 639 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 545 through 548 Processing sheet with id= N, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.340A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 764 through 766 Processing sheet with id= P, first strand: chain 'F' and resid 769 through 771 Processing sheet with id= Q, first strand: chain 'F' and resid 799 through 803 removed outlier: 3.525A pdb=" N ILE F 840 " --> pdb=" O SER F 799 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.420A pdb=" N CYS F 909 " --> pdb=" O ALA F 878 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 520 through 523 Processing sheet with id= T, first strand: chain 'E' and resid 546 through 548 removed outlier: 6.012A pdb=" N LEU E 588 " --> pdb=" O PHE E 547 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.275A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 765 through 771 Processing sheet with id= W, first strand: chain 'E' and resid 781 through 784 removed outlier: 6.114A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 877 through 880 removed outlier: 6.502A pdb=" N CYS E 909 " --> pdb=" O ALA E 878 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR E 880 " --> pdb=" O CYS E 909 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 911 " --> pdb=" O THR E 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 698 hydrogen bonds defined for protein. 2007 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: 5.35 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6077 1.34 - 1.46: 3026 1.46 - 1.57: 9370 1.57 - 1.69: 15 1.69 - 1.81: 139 Bond restraints: 18627 Sorted by residual: bond pdb=" C VAL E 911 " pdb=" N LEU E 912 " ideal model delta sigma weight residual 1.331 1.252 0.079 1.59e-02 3.96e+03 2.46e+01 bond pdb=" C ILE B 889 " pdb=" N LEU B 890 " ideal model delta sigma weight residual 1.331 1.229 0.102 2.07e-02 2.33e+03 2.44e+01 bond pdb=" CA ASP A 643 " pdb=" C ASP A 643 " ideal model delta sigma weight residual 1.523 1.492 0.032 1.34e-02 5.57e+03 5.59e+00 bond pdb=" CA LYS C 918 " pdb=" C LYS C 918 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.72e-02 3.38e+03 3.22e+00 bond pdb=" C4 ADP B1000 " pdb=" C5 ADP B1000 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.88e+00 ... (remaining 18622 not shown) Histogram of bond angle deviations from ideal: 98.67 - 106.16: 517 106.16 - 113.64: 10842 113.64 - 121.12: 9103 121.12 - 128.61: 4862 128.61 - 136.09: 96 Bond angle restraints: 25420 Sorted by residual: angle pdb=" N VAL B 555 " pdb=" CA VAL B 555 " pdb=" C VAL B 555 " ideal model delta sigma weight residual 112.80 106.85 5.95 1.15e+00 7.56e-01 2.68e+01 angle pdb=" N GLN B 875 " pdb=" CA GLN B 875 " pdb=" C GLN B 875 " ideal model delta sigma weight residual 110.97 115.36 -4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" N GLY A 571 " pdb=" CA GLY A 571 " pdb=" C GLY A 571 " ideal model delta sigma weight residual 113.18 121.46 -8.28 2.37e+00 1.78e-01 1.22e+01 angle pdb=" N VAL A 555 " pdb=" CA VAL A 555 " pdb=" C VAL A 555 " ideal model delta sigma weight residual 112.04 107.25 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" C GLU A 557 " pdb=" N ILE A 558 " pdb=" CA ILE A 558 " ideal model delta sigma weight residual 123.08 119.82 3.26 1.01e+00 9.80e-01 1.04e+01 ... (remaining 25415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 10646 24.36 - 48.72: 460 48.72 - 73.08: 33 73.08 - 97.44: 21 97.44 - 121.80: 2 Dihedral angle restraints: 11162 sinusoidal: 3808 harmonic: 7354 Sorted by residual: dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual 300.00 178.20 121.80 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" C5' ADP A1000 " pdb=" O5' ADP A1000 " pdb=" PA ADP A1000 " pdb=" O2A ADP A1000 " ideal model delta sinusoidal sigma weight residual -60.00 -165.05 105.05 1 2.00e+01 2.50e-03 3.02e+01 dihedral pdb=" CA ARG C 874 " pdb=" C ARG C 874 " pdb=" N GLN C 875 " pdb=" CA GLN C 875 " ideal model delta harmonic sigma weight residual -180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 11159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1674 0.033 - 0.066: 937 0.066 - 0.100: 332 0.100 - 0.133: 117 0.133 - 0.166: 15 Chirality restraints: 3075 Sorted by residual: chirality pdb=" CA PRO A 762 " pdb=" N PRO A 762 " pdb=" C PRO A 762 " pdb=" CB PRO A 762 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" C4' ADP B1000 " pdb=" C3' ADP B1000 " pdb=" C5' ADP B1000 " pdb=" O4' ADP B1000 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB ILE E 636 " pdb=" CA ILE E 636 " pdb=" CG1 ILE E 636 " pdb=" CG2 ILE E 636 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 3072 not shown) Planarity restraints: 3261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 584 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO F 585 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 585 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 585 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 572 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C LYS A 572 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS A 572 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 573 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 849 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO F 850 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 850 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 850 " -0.030 5.00e-02 4.00e+02 ... (remaining 3258 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 418 2.69 - 3.24: 18931 3.24 - 3.79: 28590 3.79 - 4.35: 36813 4.35 - 4.90: 60270 Nonbonded interactions: 145022 Sorted by model distance: nonbonded pdb=" OG1 THR B 886 " pdb=" OH TYR A 757 " model vdw 2.133 2.440 nonbonded pdb=" O VAL E 527 " pdb=" OH TYR E 661 " model vdw 2.142 2.440 nonbonded pdb=" OE2 GLU A 671 " pdb=" OG SER A 693 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR E 771 " pdb=" O GLY E 774 " model vdw 2.183 2.440 nonbonded pdb=" O VAL C 527 " pdb=" OH TYR C 661 " model vdw 2.195 2.440 ... (remaining 145017 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 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N o \ r name CA or name C or name O or name CB )) or resid 446 or (resid 447 through 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 or (res \ id 470 and (name N or name CA or name C or name O or name CB )) or (resid 471 th \ rough 473 and (name N or name CA or name C or name O or name CB )) or resid 474 \ or (resid 475 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 493 or (resid 494 through 49 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) or re \ sid 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) o \ r resid 502 through 503 or (resid 504 through 506 and (name N or name CA or name \ C or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 an \ d (name N or name CA or name C or name O or name CB )) or resid 512 or resid 520 \ through 521 or (resid 522 and (name N or name CA or name C or name O or name CB \ )) or resid 523 through 533 or (resid 534 and (name N or name CA or name C or n \ ame O or name CB )) or resid 535 or (resid 536 through 537 and (name N or name C \ A or name C or name O or name CB )) or resid 538 through 539 or (resid 540 throu \ gh 544 and (name N or name CA or name C or name O or name CB )) or resid 545 or \ (resid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 \ through 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or (resid 554 through 558 and (name N or name CA or name C or name O or name \ CB )) or (resid 571 through 575 and (name N or name CA or name C or name O or n \ ame CB )) or resid 576 or (resid 577 through 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 585 or (resid 586 through 588 and \ (name N or name CA or name C or name O or name CB )) or resid 589 through 590 o \ r (resid 591 through 612 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 618 through 626 and (name N or name CA or name C or name O or name C \ B )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or \ name O or name CB )) or resid 630 through 631 or (resid 632 and (name N or name \ CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 639 or (resid 640 \ and (name N or name CA or name C or name O or name CB )) or resid 641 through 64 \ 3 or (resid 644 and (name N or name CA or name C or name O or name CB )) or resi \ d 645 through 646 or (resid 647 and (name N or name CA or name C or name O or na \ me CB )) or resid 648 through 649 or (resid 650 through 652 and (name N or name \ CA or name C or name O or name CB )) or resid 653 or (resid 654 through 655 and \ (name N or name CA or name C or name O or name CB )) or resid 656 through 664 or \ (resid 665 through 666 and (name N or name CA or name C or name O or name CB )) \ or resid 667 through 668 or (resid 669 through 673 and (name N or name CA or na \ me C or name O or name CB )) or resid 674 through 676 or (resid 677 through 678 \ and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 3 or (resid 684 through 686 and (name N or name CA or name C or name O or name C \ B )) or resid 687 or resid 692 through 694 or (resid 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 through 702 or (resid 703 and (na \ me N or name CA or name C or name O or name CB )) or resid 704 or (resid 705 thr \ ough 706 and (name N or name CA or name C or name O or name CB )) or resid 707 t \ hrough 709 or (resid 710 and (name N or name CA or name C or name O or name CB ) \ ) or resid 711 through 721 or (resid 722 and (name N or name CA or name C or nam \ e O or name CB )) or resid 723 through 725 or (resid 726 and (name N or name CA \ or name C or name O or name CB )) or resid 727 through 731 or (resid 741 and (na \ me N or name CA or name C or name O or name CB )) or resid 742 or (resid 743 thr \ ough 744 and (name N or name CA or name C or name O or name CB )) or resid 745 t \ hrough 747 or (resid 748 and (name N or name CA or name C or name O or name CB ) \ ) or resid 749 through 751 or (resid 752 through 755 and (name N or name CA or n \ ame C or name O or name CB )) or resid 756 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 786 or (resid \ 787 through 791 and (name N or name CA or name C or name O or name CB )) or res \ id 798 through 800 or (resid 801 and (name N or name CA or name C or name O or n \ ame CB )) or resid 802 through 804 or (resid 805 and (name N or name CA or name \ C or name O or name CB )) or resid 806 through 821 or (resid 822 through 823 and \ (name N or name CA or name C or name O or name CB )) or resid 824 through 825 o \ r (resid 826 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 27 through 832 or (resid 833 and (name N or name CA or name C or name O or name \ CB )) or resid 834 through 836 or (resid 837 and (name N or name CA or name C or \ name O or name CB )) or resid 838 through 850 or (resid 851 and (name N or name \ CA or name C or name O or name CB )) or resid 852 through 870 or (resid 871 and \ (name N or name CA or name C or name O or name CB )) or resid 872 through 874 o \ r (resid 875 through 876 and (name N or name CA or name C or name O or name CB ) \ ) or resid 877 through 884 or (resid 885 through 886 and (name N or name CA or n \ ame C or name O or name CB )) or resid 887 or (resid 888 and (name N or name CA \ or name C or name O or name CB )) or resid 889 through 895 or (resid 896 and (na \ me N or name CA or name C or name O or name CB )) or resid 897 or (resid 898 and \ (name N or name CA or name C or name O or name CB )) or resid 899 through 916 o \ r (resid 917 through 918 and (name N or name CA or name C or name O or name CB ) \ ) or resid 919 through 921 or (resid 922 and (name N or name CA or name C or nam \ e O or name CB )) or resid 923 through 928 or (resid 929 and (name N or name CA \ or name C or name O or name CB )) or resid 930 through 936 or (resid 937 through \ 938 and (name N or name CA or name C or name O or name CB )) or resid 939 throu \ gh 947 or resid 1000)) selection = (chain 'B' and (resid 421 through 432 or (resid 433 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 446 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 or (resid 470 and (name \ N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 throu \ gh 473 and (name N or name CA or name C or name O or name CB )) or resid 474 or \ (resid 475 through 483 and (name N or name CA or name C or name O or name CB )) \ or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or nam \ e C or name O or name CB )) or resid 491 through 493 or (resid 494 through 496 a \ nd (name N or name CA or name C or name O or name CB )) or resid 497 through 498 \ or (resid 499 and (name N or name CA or name C or name O or name CB )) or resid \ 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or r \ esid 502 through 503 or (resid 504 through 506 and (name N or name CA or name C \ or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 and ( \ name N or name CA or name C or name O or name CB )) or resid 512 or resid 520 th \ rough 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) \ or resid 523 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 through 537 and (name N or name CA o \ r name C or name O or name CB )) or resid 538 through 539 or (resid 540 through \ 544 and (name N or name CA or name C or name O or name CB )) or resid 545 throug \ h 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ (resid 554 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 571 or (resid 572 through 575 and (name N or name CA or name C or name \ O or name CB )) or resid 576 or (resid 577 through 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 585 or (resid 586 through 5 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 589 through \ 591 or (resid 592 through 612 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 618 through 626 and (name N or name CA or name C or name O or \ name CB )) or resid 627 or (resid 628 through 629 and (name N or name CA or name \ C or name O or name CB )) or resid 630 through 631 or (resid 632 and (name N or \ name CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB )) or resid 635 through 639 or (resi \ d 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thro \ ugh 646 or (resid 647 and (name N or name CA or name C or name O or name CB )) o \ r resid 648 through 650 or (resid 651 through 652 and (name N or name CA or name \ C or name O or name CB )) or resid 653 or (resid 654 through 655 and (name N or \ name CA or name C or name O or name CB )) or resid 656 through 665 or (resid 66 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 667 through \ 668 or (resid 669 through 673 and (name N or name CA or name C or name O or name \ CB )) or resid 674 through 676 or (resid 677 through 678 and (name N or name CA \ or name C or name O or name CB )) or resid 679 through 683 or (resid 684 throug \ h 686 and (name N or name CA or name C or name O or name CB )) or resid 687 or r \ esid 692 through 694 or (resid 695 and (name N or name CA or name C or name O or \ name CB )) or resid 696 through 702 or (resid 703 and (name N or name CA or nam \ e C or name O or name CB )) or resid 704 or (resid 705 through 706 and (name N o \ r name CA or name C or name O or name CB )) or resid 707 through 709 or (resid 7 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 711 through \ 716 or (resid 717 and (name N or name CA or name C or name O or name CB )) or r \ esid 718 through 721 or (resid 722 and (name N or name CA or name C or name O or \ name CB )) or resid 723 through 730 or (resid 731 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 741 and (name N or name CA or name C or na \ me O or name CB )) or resid 742 or (resid 743 through 744 and (name N or name CA \ or name C or name O or name CB )) or resid 745 through 747 or (resid 748 and (n \ ame N or name CA or name C or name O or name CB )) or resid 749 through 751 or ( \ resid 752 through 755 and (name N or name CA or name C or name O or name CB )) o \ r resid 756 through 772 or (resid 773 and (name N or name CA or name C or name O \ or name CB )) or resid 774 through 786 or (resid 787 through 791 and (name N or \ name CA or name C or name O or name CB )) or resid 798 through 804 or (resid 80 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 806 through \ 825 or (resid 826 and (name N or name CA or name C or name O or name CB )) or re \ sid 827 through 832 or (resid 833 and (name N or name CA or name C or name O or \ name CB )) or resid 834 through 836 or (resid 837 and (name N or name CA or name \ C or name O or name CB )) or resid 838 through 850 or (resid 851 and (name N or \ name CA or name C or name O or name CB )) or resid 852 through 870 or (resid 87 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 872 through \ 874 or (resid 875 through 876 and (name N or name CA or name C or name O or name \ CB )) or resid 877 through 884 or (resid 885 through 886 and (name N or name CA \ or name C or name O or name CB )) or resid 887 or (resid 888 and (name N or nam \ e CA or name C or name O or name CB )) or resid 889 through 895 or (resid 896 an \ d (name N or name CA or name C or name O or name CB )) or resid 897 or (resid 89 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 899 through \ 921 or (resid 922 and (name N or name CA or name C or name O or name CB )) or re \ sid 923 through 937 or (resid 938 and (name N or name CA or name C or name O or \ name CB )) or resid 939 through 947 or resid 1000)) selection = (chain 'C' and ((resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 through 462 or (resid 463 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 474 or (resid 4 \ 75 through 483 and (name N or name CA or name C or name O or name CB )) or resid \ 484 through 488 or (resid 489 through 490 and (name N or name CA or name C or n \ ame O or name CB )) or resid 491 through 493 or (resid 494 through 496 and (name \ N or name CA or name C or name O or name CB )) or resid 497 through 498 or (res \ id 499 and (name N or name CA or name C or name O or name CB )) or resid 500 or \ (resid 501 and (name N or name CA or name C or name O or name CB )) or resid 502 \ through 504 or (resid 505 through 506 and (name N or name CA or name C or name \ O or name CB )) or resid 507 through 508 or (resid 509 through 511 and (name N o \ r name CA or name C or name O or name CB )) or resid 512 or resid 520 through 53 \ 3 or (resid 534 and (name N or name CA or name C or name O or name CB )) or resi \ d 535 through 540 or (resid 541 through 544 and (name N or name CA or name C or \ name O or name CB )) or resid 545 through 548 or (resid 549 and (name N or name \ CA or name C or name O or name CB )) or (resid 554 through 558 and (name N or na \ me CA or name C or name O or name CB )) or (resid 571 through 575 and (name N or \ name CA or name C or name O or name CB )) or resid 576 or (resid 577 through 58 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 585 or (resid 586 through 588 and (name N or name CA or name C or name O or name \ CB )) or resid 589 through 591 or (resid 592 through 612 and (name N or name CA \ or name C or name O or name CB )) or (resid 618 through 626 and (name N or name \ CA or name C or name O or name CB )) or resid 627 through 643 or (resid 644 and \ (name N or name CA or name C or name O or name CB )) or resid 645 through 671 o \ r (resid 672 through 673 and (name N or name CA or name C or name O or name CB ) \ ) or resid 674 through 694 or (resid 695 and (name N or name CA or name C or nam \ e O or name CB )) or resid 696 through 800 or (resid 801 and (name N or name CA \ or name C or name O or name CB )) or resid 802 through 821 or (resid 822 through \ 823 and (name N or name CA or name C or name O or name CB )) or resid 824 throu \ gh 825 or (resid 826 and (name N or name CA or name C or name O or name CB )) or \ resid 827 through 832 or (resid 833 and (name N or name CA or name C or name O \ or name CB )) or resid 834 through 870 or (resid 871 and (name N or name CA or n \ ame C or name O or name CB )) or resid 872 through 874 or (resid 875 through 876 \ and (name N or name CA or name C or name O or name CB )) or resid 877 through 8 \ 84 or (resid 885 through 886 and (name N or name CA or name C or name O or name \ CB )) or resid 887 through 897 or (resid 898 and (name N or name CA or name C or \ name O or name CB )) or resid 899 through 928 or (resid 929 and (name N or name \ CA or name C or name O or name CB )) or resid 930 through 937 or (resid 938 and \ (name N or name CA or name C or name O or name CB )) or resid 939 or (resid 940 \ and (name N or name CA or name C or name O or name CB )) or resid 941 through 9 \ 47 or resid 1000)) selection = (chain 'E' and (resid 421 through 433 or (resid 434 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 446 through 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 472 or (resid 4 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 474 through \ 494 or (resid 495 through 496 and (name N or name CA or name C or name O or nam \ e CB )) or resid 497 through 502 or (resid 503 through 506 and (name N or name C \ A or name C or name O or name CB )) or resid 507 through 521 or (resid 522 and ( \ name N or name CA or name C or name O or name CB )) or resid 523 through 535 or \ (resid 536 through 537 and (name N or name CA or name C or name O or name CB )) \ or resid 538 through 558 or resid 571 through 581 or (resid 582 through 583 and \ (name N or name CA or name C or name O or name CB )) or resid 584 through 589 or \ (resid 590 through 595 and (name N or name CA or name C or name O or name CB )) \ or (resid 603 through 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or n \ ame O or name CB )) or resid 630 through 631 or (resid 632 and (name N or name C \ A or name C or name O or name CB )) or resid 633 or (resid 634 and (name N or na \ me CA or name C or name O or name CB )) or resid 635 through 639 or (resid 640 a \ nd (name N or name CA or name C or name O or name CB )) or resid 641 through 642 \ or (resid 643 through 644 and (name N or name CA or name C or name O or name CB \ )) or resid 645 through 653 or (resid 654 through 655 and (name N or name CA or \ name C or name O or name CB )) or resid 656 through 664 or (resid 665 through 6 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 667 through \ 668 or (resid 669 through 673 and (name N or name CA or name C or name O or nam \ e CB )) or resid 674 through 676 or (resid 677 through 678 and (name N or name C \ A or name C or name O or name CB )) or resid 679 through 683 or (resid 684 throu \ gh 686 and (name N or name CA or name C or name O or name CB )) or resid 687 or \ resid 692 through 702 or (resid 703 and (name N or name CA or name C or name O o \ r name CB )) or resid 704 or (resid 705 through 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 709 or (resid 710 and (name N \ or name CA or name C or name O or name CB )) or resid 711 through 716 or (resid \ 717 and (name N or name CA or name C or name O or name CB )) or resid 718 throug \ h 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 725 or (resid 726 and (name N or name CA or name C or name O o \ r name CB )) or resid 727 through 730 or (resid 731 and (name N or name CA or na \ me C or name O or name CB )) or (resid 741 and (name N or name CA or name C or n \ ame O or name CB )) or resid 742 through 743 or (resid 744 and (name N or name C \ A or name C or name O or name CB )) or resid 745 through 747 or (resid 748 and ( \ name N or name CA or name C or name O or name CB )) or resid 749 through 751 or \ (resid 752 through 755 and (name N or name CA or name C or name O or name CB )) \ or resid 756 through 772 or (resid 773 and (name N or name CA or name C or name \ O or name CB )) or resid 774 through 786 or (resid 787 through 795 and (name N o \ r name CA or name C or name O or name CB )) or resid 798 through 800 or (resid 8 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 802 through \ 804 or (resid 805 and (name N or name CA or name C or name O or name CB )) or r \ esid 806 through 845 or (resid 846 and (name N or name CA or name C or name O or \ name CB )) or resid 847 through 850 or (resid 851 and (name N or name CA or nam \ e C or name O or name CB )) or resid 852 through 874 or (resid 875 through 876 a \ nd (name N or name CA or name C or name O or name CB )) or resid 877 through 885 \ or (resid 886 and (name N or name CA or name C or name O or name CB )) or resid \ 887 through 895 or (resid 896 and (name N or name CA or name C or name O or nam \ e CB )) or resid 897 through 921 or (resid 922 and (name N or name CA or name C \ or name O or name CB )) or resid 923 through 947 or resid 1000)) selection = (chain 'F' and ((resid 421 through 430 and (name N or name CA or name C or name \ O or name CB )) or resid 431 or (resid 432 through 445 and (name N or name CA or \ name C or name O or name CB )) or resid 446 or (resid 447 through 468 and (name \ N or name CA or name C or name O or name CB )) or resid 469 or (resid 470 and ( \ name N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 t \ hrough 473 and (name N or name CA or name C or name O or name CB )) or resid 474 \ or (resid 475 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 through 488 or (resid 489 through 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 493 or (resid 494 through 4 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 503 or (resid 504 through 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 508 or (resid 509 through 511 a \ nd (name N or name CA or name C or name O or name CB )) or resid 512 or resid 52 \ 0 through 521 or (resid 522 and (name N or name CA or name C or name O or name C \ B )) or resid 523 through 535 or (resid 536 through 537 and (name N or name CA o \ r name C or name O or name CB )) or resid 538 through 539 or (resid 540 through \ 544 and (name N or name CA or name C or name O or name CB )) or resid 545 or (re \ sid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 th \ rough 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) \ or (resid 554 through 558 and (name N or name CA or name C or name O or name CB \ )) or resid 571 or (resid 572 through 575 and (name N or name CA or name C or n \ ame O or name CB )) or resid 576 or (resid 577 through 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 throu \ gh 588 and (name N or name CA or name C or name O or name CB )) or resid 589 or \ (resid 590 through 612 and (name N or name CA or name C or name O or name CB )) \ or (resid 618 through 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 or (resid 628 through 629 and (name N or name CA or name C or na \ me O or name CB )) or resid 630 through 633 or (resid 634 and (name N or name CA \ or name C or name O or name CB )) or resid 635 through 639 or (resid 640 and (n \ ame N or name CA or name C or name O or name CB )) or resid 641 through 642 or ( \ resid 643 through 644 and (name N or name CA or name C or name O or name CB )) o \ r resid 645 through 646 or (resid 647 and (name N or name CA or name C or name O \ or name CB )) or resid 648 through 650 or (resid 651 through 652 and (name N or \ name CA or name C or name O or name CB )) or resid 653 or (resid 654 through 65 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 656 through \ 664 or (resid 665 through 666 and (name N or name CA or name C or name O or name \ CB )) or resid 667 through 668 or (resid 669 through 673 and (name N or name CA \ or name C or name O or name CB )) or resid 674 through 676 or (resid 677 throug \ h 678 and (name N or name CA or name C or name O or name CB )) or resid 679 thro \ ugh 683 or (resid 684 through 686 and (name N or name CA or name C or name O or \ name CB )) or resid 687 or resid 692 through 694 or (resid 695 and (name N or na \ me CA or name C or name O or name CB )) or resid 696 through 702 or (resid 703 a \ nd (name N or name CA or name C or name O or name CB )) or resid 704 or (resid 7 \ 05 through 706 and (name N or name CA or name C or name O or name CB )) or resid \ 707 through 709 or (resid 710 and (name N or name CA or name C or name O or nam \ e CB )) or resid 711 through 716 or (resid 717 and (name N or name CA or name C \ or name O or name CB )) or resid 718 through 721 or (resid 722 and (name N or na \ me CA or name C or name O or name CB )) or resid 723 through 725 or (resid 726 a \ nd (name N or name CA or name C or name O or name CB )) or resid 727 through 730 \ or (resid 731 and (name N or name CA or name C or name O or name CB )) or (resi \ d 741 and (name N or name CA or name C or name O or name CB )) or resid 742 or ( \ resid 743 through 744 and (name N or name CA or name C or name O or name CB )) o \ r resid 745 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 751 or (resid 752 through 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 772 or (resid 77 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 786 or (resid 787 through 791 and (name N or name CA or name C or name O or name \ CB )) or resid 798 through 800 or (resid 801 and (name N or name CA or name C o \ r name O or name CB )) or resid 802 through 804 or (resid 805 and (name N or nam \ e CA or name C or name O or name CB )) or resid 806 through 825 or (resid 826 an \ d (name N or name CA or name C or name O or name CB )) or resid 827 through 836 \ or (resid 837 and (name N or name CA or name C or name O or name CB )) or resid \ 838 through 850 or (resid 851 and (name N or name CA or name C or name O or name \ CB )) or resid 852 through 870 or (resid 871 and (name N or name CA or name C o \ r name O or name CB )) or resid 872 through 875 or (resid 876 and (name N or nam \ e CA or name C or name O or name CB )) or resid 877 through 884 or (resid 885 th \ rough 886 and (name N or name CA or name C or name O or name CB )) or resid 887 \ or (resid 888 and (name N or name CA or name C or name O or name CB )) or resid \ 889 through 895 or (resid 896 and (name N or name CA or name C or name O or name \ CB )) or resid 897 or (resid 898 and (name N or name CA or name C or name O or \ name CB )) or resid 899 through 914 or (resid 915 and (name N or name CA or name \ C or name O or name CB )) or resid 916 or (resid 917 through 918 and (name N or \ name CA or name C or name O or name CB )) or resid 919 through 921 or (resid 92 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 923 through \ 936 or (resid 937 through 938 and (name N or name CA or name C or name O or name \ CB )) or resid 939 through 947 or resid 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 87 5.16 5 C 11611 2.51 5 N 3162 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 2.930 Check model and map are aligned: 0.280 Process input model: 45.970 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.102 18627 Z= 0.479 Angle : 0.776 9.130 25420 Z= 0.417 Chirality : 0.047 0.166 3075 Planarity : 0.005 0.057 3261 Dihedral : 14.074 121.800 6408 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 0.12 % 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: -3.52 (0.14), residues: 2515 helix: -1.77 (0.13), residues: 1125 sheet: -2.30 (0.25), residues: 322 loop : -2.89 (0.16), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 250 average time/residue: 0.2920 time to fit residues: 110.9337 Evaluate side-chains 186 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1527 time to fit residues: 3.0347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 148 optimal weight: 0.0470 chunk 230 optimal weight: 10.0000 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: