Starting phenix.real_space_refine (version: dev) on Sat Feb 25 03:26:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/02_2023/7eos_31229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/02_2023/7eos_31229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/02_2023/7eos_31229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/02_2023/7eos_31229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/02_2023/7eos_31229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eos_31229/02_2023/7eos_31229.pdb" } resolution = 3.9 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= 0.000 sd= 0.002 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 None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24600 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6007 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6167 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6007 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6167 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.33, per 1000 atoms: 0.54 Number of scatterers: 24600 At special positions: 0 Unit cell: (120.91, 148.73, 188.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4570 8.00 N 4120 7.00 C 15760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 800 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 800 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.04 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " distance=2.03 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 340 " " NAG A 902 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 276 " " NAG B 903 " - " ASN B 368 " " NAG B 904 " - " ASN B 471 " " NAG B 905 " - " ASN B 771 " " NAG B 906 " - " ASN B 203 " " NAG B 907 " - " ASN B 239 " " NAG C 901 " - " ASN C 340 " " NAG C 902 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 368 " " NAG D 904 " - " ASN D 471 " " NAG D 905 " - " ASN D 771 " " NAG D 906 " - " ASN D 203 " " NAG D 907 " - " ASN D 239 " Time building additional restraints: 11.04 Conformation dependent library (CDL) restraints added in 3.8 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 24 sheets defined 42.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.657A pdb=" N ARG A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 106 through 121 removed outlier: 4.473A pdb=" N ALA A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.773A pdb=" N VAL A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 Processing helix chain 'A' and resid 459 through 472 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 522 removed outlier: 4.130A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 579 removed outlier: 4.057A pdb=" N VAL A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.791A pdb=" N TRP A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 653 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.817A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 removed outlier: 3.739A pdb=" N TYR A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 676' Processing helix chain 'A' and resid 689 through 698 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.906A pdb=" N LYS A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 770 through 786 removed outlier: 4.596A pdb=" N GLN A 774 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.131A pdb=" N ALA A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.675A pdb=" N SER B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.098A pdb=" N VAL B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 256 through 262 removed outlier: 4.251A pdb=" N ARG B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 296 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.022A pdb=" N GLU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.894A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 657 removed outlier: 3.614A pdb=" N ILE B 631 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 700 through 707 removed outlier: 4.059A pdb=" N ARG B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 768 through 782 removed outlier: 3.986A pdb=" N SER B 775 " --> pdb=" O ASN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.792A pdb=" N ARG B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 843 removed outlier: 3.559A pdb=" N HIS B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.533A pdb=" N ARG C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.616A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 116 " --> pdb=" O MET C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.817A pdb=" N VAL C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 459 through 472 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 515 through 522 removed outlier: 4.115A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 579 removed outlier: 4.034A pdb=" N VAL C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.784A pdb=" N TRP C 609 " --> pdb=" O ILE C 605 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 652 Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.806A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 removed outlier: 3.730A pdb=" N TYR C 676 " --> pdb=" O PRO C 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 676' Processing helix chain 'C' and resid 688 through 698 removed outlier: 4.004A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 708 removed outlier: 3.902A pdb=" N LYS C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 770 through 786 removed outlier: 4.570A pdb=" N GLN C 774 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 796 Processing helix chain 'C' and resid 814 through 837 removed outlier: 4.142A pdb=" N ALA C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 825 " --> pdb=" O PHE C 821 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 52 Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.653A pdb=" N SER D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 159 removed outlier: 4.078A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 256 through 262 removed outlier: 4.260A pdb=" N ARG D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 296 Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 381 through 385 removed outlier: 4.028A pdb=" N GLU D 385 " --> pdb=" O PRO D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.901A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 584 Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.677A pdb=" N ILE D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 695 Processing helix chain 'D' and resid 700 through 707 removed outlier: 4.048A pdb=" N ARG D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.988A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.784A pdb=" N ARG D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 843 removed outlier: 3.566A pdb=" N HIS D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 73 removed outlier: 6.738A pdb=" N ASN A 35 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 99 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 125 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.259A pdb=" N LEU A 172 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 256 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 229 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.927A pdb=" N ASP A 523 " --> pdb=" O LEU A 765 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 420 removed outlier: 3.818A pdb=" N CYS A 455 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 450 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 440 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 438 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 683 removed outlier: 6.374A pdb=" N GLY A 683 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ASP A 731 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 537 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 748 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.057A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.527A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 164 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 220 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 271 removed outlier: 4.286A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 402 removed outlier: 3.675A pdb=" N LEU B 398 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 475 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 435 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N LEU B 478 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR B 437 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 487 through 488 removed outlier: 4.558A pdb=" N GLU B 497 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 681 through 682 removed outlier: 3.999A pdb=" N ALA B 682 " --> pdb=" O ALA B 728 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 730 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLN B 536 " --> pdb=" O PHE B 753 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE B 753 " --> pdb=" O GLN B 536 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 538 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU B 751 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 540 " --> pdb=" O THR B 749 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 747 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 68 through 72 removed outlier: 6.696A pdb=" N ASN C 35 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 99 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 37 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 125 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 204 through 205 removed outlier: 6.250A pdb=" N LEU C 172 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 256 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 229 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 478 through 479 removed outlier: 3.930A pdb=" N ASP C 523 " --> pdb=" O LEU C 765 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 420 removed outlier: 3.817A pdb=" N CYS C 455 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 450 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 440 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 438 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AB9, first strand: chain 'C' and resid 682 through 683 removed outlier: 6.371A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 537 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 61 through 66 removed outlier: 3.937A pdb=" N ILE D 29 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.562A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 164 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 220 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 267 through 271 removed outlier: 4.299A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 397 through 402 removed outlier: 3.691A pdb=" N LEU D 398 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 475 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE D 435 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LEU D 478 " --> pdb=" O ILE D 435 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR D 437 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 487 through 488 removed outlier: 4.500A pdb=" N GLU D 497 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 681 through 682 removed outlier: 3.997A pdb=" N ALA D 682 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 730 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLN D 536 " --> pdb=" O PHE D 753 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE D 753 " --> pdb=" O GLN D 536 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 540 " --> pdb=" O THR D 749 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 747 " --> pdb=" O VAL D 542 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2892 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: 13.90 Time building geometry restraints manager: 11.24 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: 7858 1.34 - 1.46: 5880 1.46 - 1.58: 11160 1.58 - 1.70: 0 1.70 - 1.81: 256 Bond restraints: 25154 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.426 1.488 -0.062 3.20e-02 9.77e+02 3.72e+00 bond pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " ideal model delta sigma weight residual 1.426 1.487 -0.061 3.20e-02 9.77e+02 3.65e+00 bond pdb=" N PHE B 558 " pdb=" CA PHE B 558 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.18e-01 bond pdb=" C ARG D 659 " pdb=" N PRO D 660 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.82e-01 bond pdb=" C ARG B 659 " pdb=" N PRO B 660 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.73e-01 ... (remaining 25149 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.26: 887 107.26 - 113.96: 14337 113.96 - 120.66: 9927 120.66 - 127.36: 8669 127.36 - 134.05: 292 Bond angle restraints: 34112 Sorted by residual: angle pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C5 NAG B 901 " ideal model delta sigma weight residual 113.34 118.97 -5.63 1.74e+00 3.30e-01 1.05e+01 angle pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " pdb=" C5 NAG D 901 " ideal model delta sigma weight residual 113.34 118.89 -5.55 1.74e+00 3.30e-01 1.02e+01 angle pdb=" C MET D 394 " pdb=" N SER D 395 " pdb=" CA SER D 395 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.53e+00 angle pdb=" C MET B 394 " pdb=" N SER B 395 " pdb=" CA SER B 395 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.46e+00 angle pdb=" C GLY C 41 " pdb=" N HIS C 42 " pdb=" CA HIS C 42 " ideal model delta sigma weight residual 122.46 125.22 -2.76 1.41e+00 5.03e-01 3.82e+00 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.11: 14402 20.11 - 40.22: 469 40.22 - 60.32: 42 60.32 - 80.43: 1 80.43 - 100.54: 4 Dihedral angle restraints: 14918 sinusoidal: 5924 harmonic: 8994 Sorted by residual: dihedral pdb=" C1 NAG B 901 " pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C4 NAG B 901 " ideal model delta sinusoidal sigma weight residual -50.00 50.54 -100.54 1 2.00e+01 2.50e-03 2.84e+01 dihedral pdb=" C1 NAG D 901 " pdb=" C5 NAG D 901 " pdb=" O5 NAG D 901 " pdb=" C4 NAG D 901 " ideal model delta sinusoidal sigma weight residual -50.00 50.47 -100.47 1 2.00e+01 2.50e-03 2.84e+01 dihedral pdb=" C2 NAG D 901 " pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " pdb=" C5 NAG D 901 " ideal model delta sinusoidal sigma weight residual -50.00 44.22 -94.22 1 2.00e+01 2.50e-03 2.58e+01 ... (remaining 14915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3318 0.055 - 0.109: 517 0.109 - 0.164: 69 0.164 - 0.219: 0 0.219 - 0.274: 2 Chirality restraints: 3906 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 340 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 340 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG D 901 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D 901 " pdb=" O5 NAG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 3903 not shown) Planarity restraints: 4314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 390 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 391 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 390 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO C 391 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 139 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 140 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.015 5.00e-02 4.00e+02 ... (remaining 4311 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5191 2.78 - 3.31: 24365 3.31 - 3.84: 39025 3.84 - 4.37: 42673 4.37 - 4.90: 74695 Nonbonded interactions: 185949 Sorted by model distance: nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.254 2.440 nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.263 2.440 nonbonded pdb=" O GLU D 80 " pdb=" OG SER D 84 " model vdw 2.270 2.440 nonbonded pdb=" O GLU B 80 " pdb=" OG SER B 84 " model vdw 2.278 2.440 nonbonded pdb=" O PHE C 680 " pdb=" OH TYR C 704 " model vdw 2.285 2.440 ... (remaining 185944 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 15760 2.51 5 N 4120 2.21 5 O 4570 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: 0.780 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: 5.590 Check model and map are aligned: 0.330 Process input model: 70.140 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.001 0.062 25154 Z= 0.098 Angle : 0.399 6.823 34112 Z= 0.203 Chirality : 0.040 0.274 3906 Planarity : 0.002 0.031 4296 Dihedral : 9.125 100.538 9056 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.79 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 3066 helix: 1.89 (0.15), residues: 1262 sheet: 0.46 (0.29), residues: 372 loop : -1.24 (0.17), residues: 1432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 351 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 15 residues processed: 398 average time/residue: 0.3730 time to fit residues: 231.3686 Evaluate side-chains 225 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 2.682 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2011 time to fit residues: 9.4908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 367 ASN B 477 HIS ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN D 477 HIS D 696 GLN D 710 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 25154 Z= 0.424 Angle : 0.723 12.895 34112 Z= 0.376 Chirality : 0.046 0.266 3906 Planarity : 0.005 0.041 4296 Dihedral : 5.684 101.938 3422 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.74 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 3066 helix: 1.60 (0.15), residues: 1256 sheet: -0.27 (0.26), residues: 452 loop : -1.31 (0.18), residues: 1358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 180 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 34 residues processed: 244 average time/residue: 0.3519 time to fit residues: 139.4992 Evaluate side-chains 198 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 2.939 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2263 time to fit residues: 18.3437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 GLN B 710 ASN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 25154 Z= 0.280 Angle : 0.579 10.251 34112 Z= 0.298 Chirality : 0.043 0.245 3906 Planarity : 0.004 0.036 4296 Dihedral : 5.650 101.099 3422 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.88 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 3066 helix: 1.48 (0.15), residues: 1252 sheet: -0.46 (0.25), residues: 458 loop : -1.42 (0.18), residues: 1356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 24 residues processed: 224 average time/residue: 0.3522 time to fit residues: 127.7299 Evaluate side-chains 183 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2430 time to fit residues: 14.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 6.9990 chunk 210 optimal weight: 40.0000 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 188 optimal weight: 0.0980 chunk 281 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 266 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 25154 Z= 0.225 Angle : 0.563 11.778 34112 Z= 0.286 Chirality : 0.043 0.253 3906 Planarity : 0.003 0.037 4296 Dihedral : 5.611 101.467 3422 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 3066 helix: 1.44 (0.15), residues: 1254 sheet: -0.60 (0.25), residues: 466 loop : -1.41 (0.18), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 194 average time/residue: 0.3654 time to fit residues: 114.6964 Evaluate side-chains 183 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 2.716 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2185 time to fit residues: 13.2008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 40.0000 chunk 267 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 25154 Z= 0.232 Angle : 0.571 12.212 34112 Z= 0.290 Chirality : 0.043 0.249 3906 Planarity : 0.003 0.036 4296 Dihedral : 5.652 101.852 3422 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 3066 helix: 1.37 (0.15), residues: 1268 sheet: -0.70 (0.25), residues: 474 loop : -1.44 (0.18), residues: 1324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 190 average time/residue: 0.3678 time to fit residues: 113.6351 Evaluate side-chains 169 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 2.898 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2833 time to fit residues: 8.2609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 137 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 25154 Z= 0.232 Angle : 0.575 12.451 34112 Z= 0.290 Chirality : 0.043 0.254 3906 Planarity : 0.003 0.038 4296 Dihedral : 5.690 102.338 3422 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.51 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 3066 helix: 1.37 (0.15), residues: 1268 sheet: -0.57 (0.26), residues: 444 loop : -1.49 (0.17), residues: 1354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 191 average time/residue: 0.3758 time to fit residues: 116.2173 Evaluate side-chains 175 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2242 time to fit residues: 9.8740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 25154 Z= 0.191 Angle : 0.578 13.110 34112 Z= 0.287 Chirality : 0.043 0.254 3906 Planarity : 0.003 0.036 4296 Dihedral : 5.644 102.286 3422 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 3066 helix: 1.40 (0.15), residues: 1268 sheet: -0.72 (0.25), residues: 470 loop : -1.45 (0.18), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 190 average time/residue: 0.3761 time to fit residues: 115.5512 Evaluate side-chains 169 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 3.156 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2335 time to fit residues: 6.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 25154 Z= 0.267 Angle : 0.620 13.738 34112 Z= 0.310 Chirality : 0.043 0.253 3906 Planarity : 0.003 0.034 4296 Dihedral : 5.793 103.195 3422 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.89 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 3066 helix: 1.33 (0.15), residues: 1268 sheet: -0.72 (0.26), residues: 444 loop : -1.50 (0.18), residues: 1354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 179 average time/residue: 0.3733 time to fit residues: 108.3376 Evaluate side-chains 164 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 2.848 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2307 time to fit residues: 8.8642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.6980 chunk 284 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 275 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 25154 Z= 0.174 Angle : 0.607 14.291 34112 Z= 0.297 Chirality : 0.043 0.257 3906 Planarity : 0.003 0.041 4296 Dihedral : 5.704 102.695 3422 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 94.00 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 3066 helix: 1.30 (0.15), residues: 1270 sheet: -0.76 (0.25), residues: 474 loop : -1.44 (0.18), residues: 1322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 172 average time/residue: 0.3836 time to fit residues: 106.2484 Evaluate side-chains 162 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 2.858 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2256 time to fit residues: 5.6447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 9.9990 chunk 292 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 282 optimal weight: 0.5980 chunk 244 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.061 25154 Z= 0.157 Angle : 0.608 14.644 34112 Z= 0.296 Chirality : 0.043 0.261 3906 Planarity : 0.003 0.040 4296 Dihedral : 5.602 102.486 3422 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.84 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 3066 helix: 1.30 (0.15), residues: 1268 sheet: -0.66 (0.25), residues: 466 loop : -1.38 (0.18), residues: 1332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 167 average time/residue: 0.3804 time to fit residues: 102.1937 Evaluate side-chains 157 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 2.612 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2024 time to fit residues: 4.3175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 ASN ** 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 = 0.3670 r_free = 0.3670 target = 0.070591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052015 restraints weight = 146124.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053342 restraints weight = 84844.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.054202 restraints weight = 60075.734| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 25154 Z= 0.238 Angle : 0.650 16.303 34112 Z= 0.317 Chirality : 0.043 0.258 3906 Planarity : 0.004 0.054 4296 Dihedral : 5.718 103.263 3422 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.69 % Favored : 93.25 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 3066 helix: 1.29 (0.15), residues: 1272 sheet: -0.80 (0.25), residues: 470 loop : -1.39 (0.18), residues: 1324 =============================================================================== Job complete usr+sys time: 3803.70 seconds wall clock time: 72 minutes 6.42 seconds (4326.42 seconds total)