Starting phenix.real_space_refine on Mon Dec 11 04:32:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e93_27954/12_2023/8e93_27954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e93_27954/12_2023/8e93_27954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e93_27954/12_2023/8e93_27954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e93_27954/12_2023/8e93_27954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e93_27954/12_2023/8e93_27954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e93_27954/12_2023/8e93_27954.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.571 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 10670 2.51 5 N 2814 2.21 5 O 3101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A GLU 739": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16664 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 5620 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PTRANS': 34, 'TRANS': 765} Chain breaks: 1 Unresolved non-hydrogen bonds: 719 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 608 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 39, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 484 Chain: "B" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5208 Classifications: {'peptide': 717} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 39, 'TRANS': 677} Chain breaks: 2 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 269 Chain: "C" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2875 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 16, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 165 Chain: "D" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2715 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 14, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 581 Unresolved non-hydrogen angles: 713 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 16, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 383 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.23, per 1000 atoms: 0.55 Number of scatterers: 16664 At special positions: 0 Unit cell: (135.248, 142.952, 186.608, 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 79 16.00 O 3101 8.00 N 2814 7.00 C 10670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.04 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.04 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.04 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.04 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " 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=3, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 901 " - " ASN A 203 " " NAG A 902 " - " ASN A 350 " " NAG A 904 " - " ASN A 239 " " NAG A 905 " - " ASN A 276 " " NAG B 901 " - " ASN B 685 " " NAG C 901 " - " ASN C 471 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 471 " " NAG G 1 " - " ASN B 337 " " NAG H 1 " - " ASN C 771 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.86 Conformation dependent library (CDL) restraints added in 3.4 seconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4318 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 29 sheets defined 42.6% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.833A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.678A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.885A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.821A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.581A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.799A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.581A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 297 removed outlier: 3.750A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 4.372A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 491 through 494 removed outlier: 4.370A pdb=" N ASN A 494 " --> pdb=" O ASN A 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 491 through 494' Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.919A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 564 through 582 removed outlier: 4.206A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 629 through 657 removed outlier: 3.581A pdb=" N GLY A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.534A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 744 removed outlier: 3.601A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 783 removed outlier: 3.627A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.690A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS A 790 " --> pdb=" O GLU A 786 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 841 removed outlier: 3.941A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 836 " --> pdb=" O PHE A 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 73 through 86 removed outlier: 4.085A pdb=" N CYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 4.105A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 4.272A pdb=" N VAL B 128 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.571A pdb=" N TYR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.546A pdb=" N VAL B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.669A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.428A pdb=" N ARG B 282 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 307 removed outlier: 3.543A pdb=" N ARG B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.865A pdb=" N ARG B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 520 removed outlier: 3.533A pdb=" N SER B 517 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 652 removed outlier: 3.818A pdb=" N MET B 628 " --> pdb=" O THR B 624 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 629 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 638 " --> pdb=" O PHE B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.645A pdb=" N ASN B 695 " --> pdb=" O ASN B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.503A pdb=" N HIS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 730 through 737 removed outlier: 3.517A pdb=" N TYR B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.599A pdb=" N ILE B 773 " --> pdb=" O TRP B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 794 removed outlier: 3.751A pdb=" N LYS B 788 " --> pdb=" O GLY B 784 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 792 " --> pdb=" O LYS B 788 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 840 removed outlier: 3.659A pdb=" N LEU B 828 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 830 " --> pdb=" O MET B 826 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.691A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.695A pdb=" N SER C 553 " --> pdb=" O SER C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 582 removed outlier: 3.707A pdb=" N GLY C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 580 " --> pdb=" O MET C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 614 removed outlier: 3.756A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY C 612 " --> pdb=" O TRP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 658 removed outlier: 3.661A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.567A pdb=" N ARG C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.927A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 710 No H-bonds generated for 'chain 'C' and resid 708 through 710' Processing helix chain 'C' and resid 713 through 722 removed outlier: 3.506A pdb=" N ARG C 722 " --> pdb=" O ILE C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 744 removed outlier: 3.669A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.587A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.755A pdb=" N TRP C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 793 " --> pdb=" O ASP C 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 470 removed outlier: 4.156A pdb=" N ARG D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.662A pdb=" N GLU D 497 " --> pdb=" O GLY D 493 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 498 " --> pdb=" O MET D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 4.121A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 576 removed outlier: 3.545A pdb=" N TRP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 567 " --> pdb=" O CYS D 563 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.928A pdb=" N VAL D 603 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 654 removed outlier: 3.871A pdb=" N VAL D 631 " --> pdb=" O ILE D 627 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 639 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER D 642 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR D 644 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 653 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 654 " --> pdb=" O PHE D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 692 removed outlier: 4.079A pdb=" N ARG D 690 " --> pdb=" O GLY D 686 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 686 through 692' Processing helix chain 'D' and resid 696 through 701 removed outlier: 4.435A pdb=" N HIS D 700 " --> pdb=" O TYR D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 4.130A pdb=" N LYS D 705 " --> pdb=" O HIS D 702 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 706 " --> pdb=" O MET D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 706' Processing helix chain 'D' and resid 711 through 721 removed outlier: 4.368A pdb=" N SER D 717 " --> pdb=" O ASP D 713 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 740 removed outlier: 4.247A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 736 " --> pdb=" O VAL D 732 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP D 740 " --> pdb=" O MET D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 783 removed outlier: 3.630A pdb=" N ALA D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 792 removed outlier: 4.345A pdb=" N LYS D 788 " --> pdb=" O GLY D 784 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 792 " --> pdb=" O LYS D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 838 removed outlier: 4.253A pdb=" N MET D 821 " --> pdb=" O GLY D 817 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 824 " --> pdb=" O TYR D 820 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA D 825 " --> pdb=" O MET D 821 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 836 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS D 837 " --> pdb=" O PHE D 833 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 838 " --> pdb=" O ALA D 834 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.063A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 196 removed outlier: 5.327A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.800A pdb=" N HIS A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.303A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.578A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 434 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.734A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AB2, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.521A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.775A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.440A pdb=" N PHE B 165 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N VAL B 199 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 167 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 164 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL B 225 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 166 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR B 227 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 168 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 274 through 277 removed outlier: 6.666A pdb=" N VAL B 360 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 407 removed outlier: 3.531A pdb=" N THR B 407 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG B 434 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417 Processing sheet with id=AB9, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AC1, first strand: chain 'B' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'B' and resid 726 through 729 removed outlier: 3.512A pdb=" N TYR B 728 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 746 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 726 through 729 removed outlier: 3.512A pdb=" N TYR B 728 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE B 531 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA B 755 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 476 through 478 removed outlier: 5.739A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.550A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 487 through 489 removed outlier: 3.675A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.289A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.289A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 473 through 477 removed outlier: 6.396A pdb=" N LEU D 403 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR D 476 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL D 405 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D 505 " --> pdb=" O THR D 404 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 414 through 417 removed outlier: 3.523A pdb=" N LEU D 452 " --> pdb=" O CYS D 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 725 through 729 removed outlier: 5.100A pdb=" N ILE D 531 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA D 755 " --> pdb=" O ILE D 531 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1842 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: 5.68 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2678 1.30 - 1.43: 4527 1.43 - 1.57: 9697 1.57 - 1.70: 2 1.70 - 1.83: 124 Bond restraints: 17028 Sorted by residual: bond pdb=" C THR B 404 " pdb=" N VAL B 405 " ideal model delta sigma weight residual 1.330 1.549 -0.218 1.26e-02 6.30e+03 3.00e+02 bond pdb=" C PRO B 388 " pdb=" O PRO B 388 " ideal model delta sigma weight residual 1.233 1.167 0.065 1.16e-02 7.43e+03 3.18e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.517 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C LEU B 403 " pdb=" O LEU B 403 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.22e-02 6.72e+03 2.98e+01 bond pdb=" C PRO B 396 " pdb=" O PRO B 396 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.24e-02 6.50e+03 2.50e+01 ... (remaining 17023 not shown) Histogram of bond angle deviations from ideal: 94.21 - 102.23: 64 102.23 - 110.24: 3602 110.24 - 118.25: 9790 118.25 - 126.26: 9563 126.26 - 134.27: 322 Bond angle restraints: 23341 Sorted by residual: angle pdb=" CA PRO C 547 " pdb=" N PRO C 547 " pdb=" CD PRO C 547 " ideal model delta sigma weight residual 112.00 97.08 14.92 1.40e+00 5.10e-01 1.14e+02 angle pdb=" C THR B 404 " pdb=" N VAL B 405 " pdb=" CA VAL B 405 " ideal model delta sigma weight residual 123.19 133.13 -9.94 1.24e+00 6.50e-01 6.42e+01 angle pdb=" C PRO B 396 " pdb=" CA PRO B 396 " pdb=" CB PRO B 396 " ideal model delta sigma weight residual 111.56 102.85 8.71 1.27e+00 6.20e-01 4.71e+01 angle pdb=" N VAL C 793 " pdb=" CA VAL C 793 " pdb=" C VAL C 793 " ideal model delta sigma weight residual 113.71 107.33 6.38 9.50e-01 1.11e+00 4.52e+01 angle pdb=" N PRO B 396 " pdb=" CD PRO B 396 " pdb=" CG PRO B 396 " ideal model delta sigma weight residual 103.20 94.21 8.99 1.50e+00 4.44e-01 3.59e+01 ... (remaining 23336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.31: 9377 23.31 - 46.63: 672 46.63 - 69.94: 90 69.94 - 93.26: 21 93.26 - 116.57: 4 Dihedral angle restraints: 10164 sinusoidal: 3477 harmonic: 6687 Sorted by residual: dihedral pdb=" CB CYS D 433 " pdb=" SG CYS D 433 " pdb=" SG CYS D 454 " pdb=" CB CYS D 454 " ideal model delta sinusoidal sigma weight residual -86.00 -172.56 86.56 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CA GLY B 40 " pdb=" C GLY B 40 " pdb=" N PRO B 41 " pdb=" CA PRO B 41 " ideal model delta harmonic sigma weight residual -180.00 -138.77 -41.23 0 5.00e+00 4.00e-02 6.80e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 798 " pdb=" CB CYS B 798 " ideal model delta sinusoidal sigma weight residual -86.00 -157.76 71.76 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 10161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2803 0.114 - 0.228: 61 0.228 - 0.342: 6 0.342 - 0.456: 4 0.456 - 0.569: 1 Chirality restraints: 2875 Sorted by residual: chirality pdb=" C1 NAG A 904 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG A 904 " pdb=" O5 NAG A 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.37e+00 chirality pdb=" CA GLU C 781 " pdb=" N GLU C 781 " pdb=" C GLU C 781 " pdb=" CB GLU C 781 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 2872 not shown) Planarity restraints: 2961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 669 " -0.112 5.00e-02 4.00e+02 1.67e-01 4.47e+01 pdb=" N PRO C 670 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO C 670 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO C 670 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 546 " -0.085 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO C 547 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO C 547 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 547 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 400 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C SER B 400 " -0.078 2.00e-02 2.50e+03 pdb=" O SER B 400 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG B 401 " 0.027 2.00e-02 2.50e+03 ... (remaining 2958 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 172 2.63 - 3.20: 15520 3.20 - 3.77: 23322 3.77 - 4.33: 29607 4.33 - 4.90: 48393 Nonbonded interactions: 117014 Sorted by model distance: nonbonded pdb=" O ASN D 612 " pdb=" ND2 ASN D 612 " model vdw 2.066 2.520 nonbonded pdb=" O MET A 125 " pdb=" NH2 ARG A 139 " model vdw 2.121 2.520 nonbonded pdb=" OG1 THR B 529 " pdb=" OD1 ASP B 729 " model vdw 2.125 2.440 nonbonded pdb=" O VAL B 128 " pdb=" NE2 GLN B 141 " model vdw 2.204 2.520 nonbonded pdb=" OE1 GLN B 213 " pdb=" NE2 GLN B 242 " model vdw 2.226 2.520 ... (remaining 117009 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 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.590 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.250 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.005 0.218 17028 Z= 0.311 Angle : 0.834 14.924 23341 Z= 0.473 Chirality : 0.050 0.569 2875 Planarity : 0.006 0.167 2951 Dihedral : 15.923 116.569 5807 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.70 % Favored : 91.26 % Rotamer: Outliers : 0.65 % Allowed : 23.97 % Favored : 75.39 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % 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: -2.88 (0.16), residues: 2300 helix: -1.02 (0.17), residues: 823 sheet: -1.79 (0.34), residues: 221 loop : -2.64 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 632 HIS 0.017 0.001 HIS B 334 PHE 0.022 0.001 PHE C 654 TYR 0.058 0.001 TYR B 390 ARG 0.007 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 242 average time/residue: 0.2226 time to fit residues: 89.9103 Evaluate side-chains 223 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 217 time to evaluate : 1.848 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1536 time to fit residues: 4.0669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17028 Z= 0.264 Angle : 0.708 10.768 23341 Z= 0.361 Chirality : 0.047 0.319 2875 Planarity : 0.005 0.106 2951 Dihedral : 8.915 86.950 2766 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.78 % Favored : 90.13 % Rotamer: Outliers : 5.10 % Allowed : 21.77 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % 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: -2.36 (0.17), residues: 2300 helix: -0.20 (0.17), residues: 865 sheet: -1.50 (0.35), residues: 229 loop : -2.72 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 792 HIS 0.017 0.001 HIS B 334 PHE 0.018 0.001 PHE D 650 TYR 0.018 0.001 TYR C 681 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 229 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 44 residues processed: 286 average time/residue: 0.2199 time to fit residues: 105.4421 Evaluate side-chains 260 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 1.882 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.1506 time to fit residues: 15.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 209 optimal weight: 6.9990 chunk 226 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN A 536 GLN B 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17028 Z= 0.291 Angle : 0.700 12.353 23341 Z= 0.354 Chirality : 0.046 0.342 2875 Planarity : 0.004 0.074 2951 Dihedral : 8.498 74.545 2766 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.26 % Favored : 89.65 % Rotamer: Outliers : 4.78 % Allowed : 22.93 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.09 % 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: -2.32 (0.17), residues: 2300 helix: -0.02 (0.17), residues: 872 sheet: -1.52 (0.34), residues: 234 loop : -2.84 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 792 HIS 0.016 0.001 HIS B 334 PHE 0.019 0.001 PHE B 634 TYR 0.015 0.001 TYR B 476 ARG 0.002 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 226 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 33 residues processed: 282 average time/residue: 0.2265 time to fit residues: 108.5489 Evaluate side-chains 239 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 1.905 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.1562 time to fit residues: 12.7709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 0.1980 chunk 157 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 199 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17028 Z= 0.216 Angle : 0.663 12.502 23341 Z= 0.332 Chirality : 0.045 0.347 2875 Planarity : 0.004 0.067 2951 Dihedral : 8.066 67.342 2766 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.83 % Favored : 90.13 % Rotamer: Outliers : 4.13 % Allowed : 24.42 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.09 % 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: -2.12 (0.17), residues: 2300 helix: 0.19 (0.18), residues: 873 sheet: -1.41 (0.34), residues: 232 loop : -2.76 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 792 HIS 0.016 0.001 HIS B 334 PHE 0.018 0.001 PHE D 635 TYR 0.013 0.001 TYR B 476 ARG 0.006 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 223 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 35 residues processed: 265 average time/residue: 0.2152 time to fit residues: 96.7375 Evaluate side-chains 248 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 1.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.1500 time to fit residues: 12.5254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 91 optimal weight: 0.0040 chunk 189 optimal weight: 9.9990 chunk 153 optimal weight: 0.0000 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17028 Z= 0.168 Angle : 0.642 12.019 23341 Z= 0.318 Chirality : 0.044 0.254 2875 Planarity : 0.004 0.064 2951 Dihedral : 7.498 57.003 2766 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.65 % Allowed : 25.13 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2300 helix: 0.35 (0.18), residues: 882 sheet: -1.28 (0.34), residues: 232 loop : -2.63 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 636 HIS 0.016 0.001 HIS B 334 PHE 0.022 0.001 PHE D 635 TYR 0.018 0.001 TYR B 476 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 15 residues processed: 273 average time/residue: 0.2059 time to fit residues: 95.8942 Evaluate side-chains 231 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 1.750 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.1551 time to fit residues: 6.7264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 116 optimal weight: 0.3980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN C 650 ASN D 612 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17028 Z= 0.256 Angle : 0.669 13.037 23341 Z= 0.331 Chirality : 0.044 0.260 2875 Planarity : 0.004 0.061 2951 Dihedral : 7.488 57.668 2766 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.49 % Allowed : 26.42 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2300 helix: 0.45 (0.18), residues: 870 sheet: -1.35 (0.33), residues: 250 loop : -2.66 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 792 HIS 0.015 0.001 HIS B 334 PHE 0.024 0.001 PHE D 635 TYR 0.026 0.001 TYR B 476 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 217 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 32 residues processed: 254 average time/residue: 0.2175 time to fit residues: 93.7558 Evaluate side-chains 242 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 1.910 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 2 residues processed: 32 average time/residue: 0.1511 time to fit residues: 11.5379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 221 optimal weight: 0.3980 chunk 138 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17028 Z= 0.174 Angle : 0.643 13.107 23341 Z= 0.316 Chirality : 0.044 0.254 2875 Planarity : 0.004 0.060 2951 Dihedral : 7.182 56.701 2766 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.68 % Allowed : 26.87 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2300 helix: 0.62 (0.18), residues: 870 sheet: -1.29 (0.34), residues: 243 loop : -2.57 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 632 HIS 0.016 0.001 HIS B 334 PHE 0.026 0.001 PHE D 635 TYR 0.020 0.001 TYR B 476 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 229 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 249 average time/residue: 0.2238 time to fit residues: 93.1920 Evaluate side-chains 223 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 1.961 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.1589 time to fit residues: 5.2766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN D 612 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17028 Z= 0.188 Angle : 0.644 11.783 23341 Z= 0.315 Chirality : 0.044 0.258 2875 Planarity : 0.004 0.062 2951 Dihedral : 7.023 56.277 2766 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.87 % Allowed : 27.91 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2300 helix: 0.70 (0.18), residues: 872 sheet: -1.20 (0.33), residues: 256 loop : -2.56 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 792 HIS 0.015 0.001 HIS B 334 PHE 0.027 0.001 PHE D 635 TYR 0.029 0.001 TYR A 647 ARG 0.006 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 240 average time/residue: 0.2235 time to fit residues: 89.9372 Evaluate side-chains 228 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 1.979 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.1480 time to fit residues: 7.2157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 193 optimal weight: 0.0040 chunk 206 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 186 optimal weight: 0.3980 chunk 195 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 overall best weight: 3.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN D 612 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17028 Z= 0.319 Angle : 0.708 11.344 23341 Z= 0.353 Chirality : 0.046 0.274 2875 Planarity : 0.004 0.065 2951 Dihedral : 7.388 59.691 2766 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 1.36 % Allowed : 28.36 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2300 helix: 0.60 (0.18), residues: 863 sheet: -1.36 (0.33), residues: 240 loop : -2.70 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 792 HIS 0.014 0.001 HIS B 334 PHE 0.026 0.002 PHE D 635 TYR 0.031 0.002 TYR B 476 ARG 0.006 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 225 average time/residue: 0.2150 time to fit residues: 82.5075 Evaluate side-chains 219 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.936 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.1767 time to fit residues: 7.8839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 151 optimal weight: 0.8980 chunk 229 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 182 optimal weight: 0.2980 chunk 18 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17028 Z= 0.179 Angle : 0.660 11.745 23341 Z= 0.322 Chirality : 0.044 0.261 2875 Planarity : 0.004 0.077 2951 Dihedral : 7.058 57.059 2766 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.58 % Allowed : 28.81 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2300 helix: 0.78 (0.18), residues: 862 sheet: -1.16 (0.34), residues: 236 loop : -2.51 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 792 HIS 0.015 0.001 HIS B 334 PHE 0.029 0.001 PHE D 635 TYR 0.022 0.001 TYR B 476 ARG 0.007 0.000 ARG B 411 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 225 average time/residue: 0.2483 time to fit residues: 92.2458 Evaluate side-chains 213 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 1.916 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.1630 time to fit residues: 4.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.3980 chunk 194 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 182 optimal weight: 0.0670 chunk 76 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN D 612 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100366 restraints weight = 40319.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099641 restraints weight = 28037.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100204 restraints weight = 26245.355| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17028 Z= 0.192 Angle : 0.664 11.333 23341 Z= 0.322 Chirality : 0.044 0.263 2875 Planarity : 0.004 0.076 2951 Dihedral : 7.136 56.864 2766 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.52 % Allowed : 29.78 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2300 helix: 0.83 (0.18), residues: 868 sheet: -1.27 (0.33), residues: 246 loop : -2.49 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 792 HIS 0.015 0.001 HIS B 334 PHE 0.031 0.001 PHE D 635 TYR 0.024 0.001 TYR B 476 ARG 0.007 0.000 ARG B 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.76 seconds wall clock time: 62 minutes 5.20 seconds (3725.20 seconds total)