Starting phenix.real_space_refine on Sun May 18 10:51:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e93_27954/05_2025/8e93_27954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e93_27954/05_2025/8e93_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/cci-nas-00/data/ceres_data/8e93_27954/05_2025/8e93_27954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e93_27954/05_2025/8e93_27954.map" model { file = "/net/cci-nas-00/data/ceres_data/8e93_27954/05_2025/8e93_27954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e93_27954/05_2025/8e93_27954.cif" } 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. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9 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: 9 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: 10.84, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 4.67 Conformation dependent library (CDL) restraints added in 2.5 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: 2.18 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: 5.46 Time building geometry restraints manager: 5.39 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: 0.00 - 2.98: 23014 2.98 - 5.97: 275 5.97 - 8.95: 43 8.95 - 11.94: 7 11.94 - 14.92: 2 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: 9390 23.31 - 46.63: 677 46.63 - 69.94: 90 69.94 - 93.26: 33 93.26 - 116.57: 12 Dihedral angle restraints: 10202 sinusoidal: 3515 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 10199 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 3.120 nonbonded pdb=" O MET A 125 " pdb=" NH2 ARG A 139 " model vdw 2.121 3.120 nonbonded pdb=" OG1 THR B 529 " pdb=" OD1 ASP B 729 " model vdw 2.125 3.040 nonbonded pdb=" O VAL B 128 " pdb=" NE2 GLN B 141 " model vdw 2.204 3.120 nonbonded pdb=" OE1 GLN B 213 " pdb=" NE2 GLN B 242 " model vdw 2.226 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 4.120 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: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.310 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- 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 17060 Z= 0.263 Angle : 0.851 14.924 23415 Z= 0.476 Chirality : 0.050 0.569 2875 Planarity : 0.006 0.167 2951 Dihedral : 16.774 116.569 5845 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 10) link_NAG-ASN : angle 3.89199 ( 30) link_BETA1-4 : bond 0.01498 ( 6) link_BETA1-4 : angle 3.00948 ( 18) hydrogen bonds : bond 0.31071 ( 637) hydrogen bonds : angle 8.69785 ( 1842) SS BOND : bond 0.00412 ( 13) SS BOND : angle 1.72133 ( 26) covalent geometry : bond 0.00452 (17028) covalent geometry : angle 0.83428 (23341) Misc. bond : bond 0.00517 ( 3) *********************** 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 to be fit. rotamer outliers: 10 poor density : 233 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9100 (pp) REVERT: B 642 SER cc_start: 0.8805 (t) cc_final: 0.8370 (p) REVERT: C 739 GLU cc_start: 0.8847 (tp30) cc_final: 0.8062 (tp30) REVERT: D 480 ASN cc_start: 0.8127 (t0) cc_final: 0.7693 (t0) outliers start: 10 outliers final: 6 residues processed: 242 average time/residue: 0.2100 time to fit residues: 84.3799 Evaluate side-chains 227 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 781 GLU 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: 1.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN B 395 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097601 restraints weight = 40145.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096605 restraints weight = 29090.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097288 restraints weight = 26449.864| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17060 Z= 0.176 Angle : 0.737 10.769 23415 Z= 0.372 Chirality : 0.047 0.320 2875 Planarity : 0.005 0.109 2951 Dihedral : 10.367 88.818 2818 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.57 % Favored : 90.39 % Rotamer: Outliers : 4.97 % Allowed : 21.96 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % 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: -2.35 (0.17), residues: 2300 helix: -0.18 (0.17), residues: 863 sheet: -1.48 (0.35), residues: 224 loop : -2.72 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 792 HIS 0.015 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 10) link_NAG-ASN : angle 3.39543 ( 30) link_BETA1-4 : bond 0.00961 ( 6) link_BETA1-4 : angle 2.93514 ( 18) hydrogen bonds : bond 0.06552 ( 637) hydrogen bonds : angle 5.65761 ( 1842) SS BOND : bond 0.00377 ( 13) SS BOND : angle 2.06909 ( 26) covalent geometry : bond 0.00397 (17028) covalent geometry : angle 0.72004 (23341) Misc. bond : bond 0.00465 ( 3) *********************** 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 312 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 235 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8288 (pp) REVERT: A 125 MET cc_start: 0.8629 (mmm) cc_final: 0.7242 (mmm) REVERT: A 545 GLU cc_start: 0.7497 (pm20) cc_final: 0.7275 (pm20) REVERT: B 153 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8880 (mp) REVERT: B 403 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9055 (pp) REVERT: C 690 ASP cc_start: 0.9113 (t70) cc_final: 0.8808 (t0) REVERT: C 739 GLU cc_start: 0.8643 (tp30) cc_final: 0.8117 (tp30) REVERT: D 477 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5751 (mt) REVERT: D 480 ASN cc_start: 0.8446 (t0) cc_final: 0.8019 (t0) REVERT: D 635 PHE cc_start: 0.8038 (t80) cc_final: 0.7710 (t80) REVERT: D 794 LEU cc_start: 0.8473 (tp) cc_final: 0.8102 (pp) REVERT: D 813 ASP cc_start: 0.8469 (t0) cc_final: 0.8193 (m-30) outliers start: 77 outliers final: 42 residues processed: 290 average time/residue: 0.2128 time to fit residues: 103.1153 Evaluate side-chains 263 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 167 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096111 restraints weight = 40198.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096312 restraints weight = 27179.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096903 restraints weight = 25169.176| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17060 Z= 0.192 Angle : 0.732 12.697 23415 Z= 0.366 Chirality : 0.047 0.343 2875 Planarity : 0.005 0.074 2951 Dihedral : 9.125 74.416 2815 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.26 % Favored : 89.70 % Rotamer: Outliers : 7.04 % Allowed : 21.64 % Favored : 71.32 % 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: -2.31 (0.17), residues: 2300 helix: -0.05 (0.17), residues: 872 sheet: -1.61 (0.33), residues: 248 loop : -2.78 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 792 HIS 0.014 0.001 HIS B 334 PHE 0.020 0.002 PHE B 634 TYR 0.016 0.001 TYR B 476 ARG 0.003 0.000 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 10) link_NAG-ASN : angle 3.33958 ( 30) link_BETA1-4 : bond 0.00883 ( 6) link_BETA1-4 : angle 2.99548 ( 18) hydrogen bonds : bond 0.05465 ( 637) hydrogen bonds : angle 5.18594 ( 1842) SS BOND : bond 0.00597 ( 13) SS BOND : angle 1.88698 ( 26) covalent geometry : bond 0.00448 (17028) covalent geometry : angle 0.71607 (23341) Misc. bond : bond 0.00386 ( 3) *********************** 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 333 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 224 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8297 (pp) REVERT: A 180 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8490 (tt) REVERT: A 455 CYS cc_start: 0.5295 (m) cc_final: 0.5011 (m) REVERT: A 487 GLN cc_start: 0.8671 (pp30) cc_final: 0.8467 (tt0) REVERT: A 545 GLU cc_start: 0.7537 (pm20) cc_final: 0.7222 (pm20) REVERT: A 639 PHE cc_start: 0.8354 (t80) cc_final: 0.7953 (t80) REVERT: A 642 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9221 (tp) REVERT: B 150 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 153 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8907 (mp) REVERT: B 403 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9043 (pp) REVERT: B 452 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8077 (pp) REVERT: B 462 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8719 (tp) REVERT: C 739 GLU cc_start: 0.8751 (tp30) cc_final: 0.8276 (tp30) REVERT: D 476 TYR cc_start: 0.7315 (t80) cc_final: 0.7070 (t80) REVERT: D 480 ASN cc_start: 0.8364 (t0) cc_final: 0.7917 (t0) REVERT: D 513 ASN cc_start: 0.7120 (p0) cc_final: 0.6871 (p0) REVERT: D 696 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5888 (m-10) REVERT: D 794 LEU cc_start: 0.8402 (tp) cc_final: 0.8108 (pp) outliers start: 109 outliers final: 71 residues processed: 305 average time/residue: 0.2038 time to fit residues: 103.1884 Evaluate side-chains 287 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 207 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 696 TYR Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 127 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 36 optimal weight: 0.0470 chunk 218 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098752 restraints weight = 40208.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099135 restraints weight = 26085.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.099365 restraints weight = 23730.434| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17060 Z= 0.129 Angle : 0.674 11.146 23415 Z= 0.333 Chirality : 0.045 0.334 2875 Planarity : 0.004 0.068 2951 Dihedral : 8.095 63.486 2810 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 6.14 % Allowed : 22.55 % Favored : 71.32 % 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: -2.06 (0.17), residues: 2300 helix: 0.18 (0.17), residues: 874 sheet: -1.53 (0.33), residues: 251 loop : -2.64 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 792 HIS 0.014 0.001 HIS B 334 PHE 0.016 0.001 PHE B 634 TYR 0.014 0.001 TYR B 303 ARG 0.005 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 10) link_NAG-ASN : angle 3.04694 ( 30) link_BETA1-4 : bond 0.00966 ( 6) link_BETA1-4 : angle 3.08790 ( 18) hydrogen bonds : bond 0.04214 ( 637) hydrogen bonds : angle 4.74009 ( 1842) SS BOND : bond 0.00454 ( 13) SS BOND : angle 1.85078 ( 26) covalent geometry : bond 0.00289 (17028) covalent geometry : angle 0.65766 (23341) Misc. bond : bond 0.00378 ( 3) *********************** 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 327 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 232 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 GLU cc_start: 0.7593 (pm20) cc_final: 0.7223 (pm20) REVERT: A 639 PHE cc_start: 0.8341 (t80) cc_final: 0.7963 (t80) REVERT: A 642 ILE cc_start: 0.9556 (OUTLIER) cc_final: 0.9227 (tp) REVERT: B 153 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8867 (mp) REVERT: B 403 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9022 (pp) REVERT: B 658 ASP cc_start: 0.7548 (m-30) cc_final: 0.6499 (p0) REVERT: C 739 GLU cc_start: 0.8670 (tp30) cc_final: 0.8264 (tp30) REVERT: D 476 TYR cc_start: 0.7157 (t80) cc_final: 0.6888 (t80) REVERT: D 480 ASN cc_start: 0.8243 (t0) cc_final: 0.7825 (t0) REVERT: D 556 TRP cc_start: 0.8312 (m100) cc_final: 0.7868 (m100) REVERT: D 759 TYR cc_start: 0.8103 (m-80) cc_final: 0.7841 (m-80) REVERT: D 794 LEU cc_start: 0.8368 (tp) cc_final: 0.8089 (pp) outliers start: 95 outliers final: 60 residues processed: 302 average time/residue: 0.2067 time to fit residues: 105.0632 Evaluate side-chains 273 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 798 CYS Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 193 optimal weight: 0.0040 chunk 28 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN D 612 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096946 restraints weight = 40717.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096534 restraints weight = 27486.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097188 restraints weight = 23210.769| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17060 Z= 0.159 Angle : 0.698 12.089 23415 Z= 0.347 Chirality : 0.045 0.259 2875 Planarity : 0.004 0.065 2951 Dihedral : 7.920 59.507 2810 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 7.11 % Allowed : 23.00 % Favored : 69.90 % 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: -1.97 (0.17), residues: 2300 helix: 0.30 (0.17), residues: 877 sheet: -1.45 (0.32), residues: 269 loop : -2.66 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 792 HIS 0.014 0.001 HIS B 334 PHE 0.026 0.001 PHE D 635 TYR 0.022 0.001 TYR B 476 ARG 0.004 0.000 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 10) link_NAG-ASN : angle 3.02166 ( 30) link_BETA1-4 : bond 0.00941 ( 6) link_BETA1-4 : angle 2.96170 ( 18) hydrogen bonds : bond 0.04348 ( 637) hydrogen bonds : angle 4.75077 ( 1842) SS BOND : bond 0.00565 ( 13) SS BOND : angle 2.29302 ( 26) covalent geometry : bond 0.00371 (17028) covalent geometry : angle 0.68161 (23341) Misc. bond : bond 0.00363 ( 3) *********************** 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 323 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 213 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 639 PHE cc_start: 0.8540 (t80) cc_final: 0.8095 (t80) REVERT: A 642 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9174 (tp) REVERT: B 153 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8858 (mp) REVERT: B 403 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9083 (pp) REVERT: B 452 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8078 (pp) REVERT: B 658 ASP cc_start: 0.7630 (m-30) cc_final: 0.6477 (p0) REVERT: C 739 GLU cc_start: 0.8760 (tp30) cc_final: 0.8349 (tp30) REVERT: D 476 TYR cc_start: 0.7381 (t80) cc_final: 0.7093 (t80) REVERT: D 480 ASN cc_start: 0.8436 (t0) cc_final: 0.8007 (t0) REVERT: D 699 MET cc_start: 0.8087 (tpt) cc_final: 0.7386 (mpp) REVERT: D 759 TYR cc_start: 0.8228 (m-80) cc_final: 0.8026 (m-80) REVERT: D 794 LEU cc_start: 0.8488 (tp) cc_final: 0.8142 (pp) outliers start: 110 outliers final: 73 residues processed: 299 average time/residue: 0.2016 time to fit residues: 101.4664 Evaluate side-chains 287 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 25 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 154 optimal weight: 40.0000 chunk 106 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN D 612 ASN D 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095846 restraints weight = 40642.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094894 restraints weight = 29443.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095659 restraints weight = 25484.526| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17060 Z= 0.224 Angle : 0.736 12.427 23415 Z= 0.368 Chirality : 0.046 0.283 2875 Planarity : 0.004 0.065 2951 Dihedral : 8.084 61.482 2810 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 7.95 % Allowed : 22.48 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.14 % 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: -2.07 (0.17), residues: 2300 helix: 0.30 (0.17), residues: 869 sheet: -1.62 (0.31), residues: 272 loop : -2.75 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 PHE 0.022 0.002 PHE D 635 TYR 0.024 0.002 TYR C 681 ARG 0.004 0.000 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 10) link_NAG-ASN : angle 3.31729 ( 30) link_BETA1-4 : bond 0.00893 ( 6) link_BETA1-4 : angle 2.88906 ( 18) hydrogen bonds : bond 0.04592 ( 637) hydrogen bonds : angle 4.84299 ( 1842) SS BOND : bond 0.00497 ( 13) SS BOND : angle 2.26361 ( 26) covalent geometry : bond 0.00526 (17028) covalent geometry : angle 0.71885 (23341) Misc. bond : bond 0.00378 ( 3) *********************** 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 329 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 206 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8567 (tt) REVERT: A 639 PHE cc_start: 0.8425 (t80) cc_final: 0.7991 (t80) REVERT: A 642 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9228 (tp) REVERT: B 150 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8671 (mp) REVERT: B 153 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8936 (mp) REVERT: B 403 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9058 (pp) REVERT: B 452 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8091 (pp) REVERT: B 658 ASP cc_start: 0.7659 (m-30) cc_final: 0.6520 (p0) REVERT: C 739 GLU cc_start: 0.8749 (tp30) cc_final: 0.8338 (tp30) REVERT: D 476 TYR cc_start: 0.7313 (t80) cc_final: 0.7030 (t80) REVERT: D 480 ASN cc_start: 0.8368 (t0) cc_final: 0.7944 (t0) REVERT: D 696 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5960 (m-10) REVERT: D 794 LEU cc_start: 0.8438 (tp) cc_final: 0.8121 (pp) outliers start: 123 outliers final: 96 residues processed: 301 average time/residue: 0.2243 time to fit residues: 114.6717 Evaluate side-chains 305 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 202 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 696 TYR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 798 CYS Chi-restraints excluded: chain D residue 814 ASN Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 199 optimal weight: 7.9990 chunk 75 optimal weight: 0.0370 chunk 55 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 208 optimal weight: 0.0970 chunk 35 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN D 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.124408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099375 restraints weight = 40341.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098948 restraints weight = 29772.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099524 restraints weight = 25711.638| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17060 Z= 0.118 Angle : 0.670 12.422 23415 Z= 0.328 Chirality : 0.044 0.283 2875 Planarity : 0.004 0.064 2951 Dihedral : 7.507 56.781 2810 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 5.36 % Allowed : 25.26 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2300 helix: 0.53 (0.18), residues: 873 sheet: -1.29 (0.34), residues: 236 loop : -2.56 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 PHE 0.024 0.001 PHE D 635 TYR 0.024 0.001 TYR D 759 ARG 0.002 0.000 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 10) link_NAG-ASN : angle 2.98884 ( 30) link_BETA1-4 : bond 0.01052 ( 6) link_BETA1-4 : angle 2.93854 ( 18) hydrogen bonds : bond 0.03658 ( 637) hydrogen bonds : angle 4.44435 ( 1842) SS BOND : bond 0.00358 ( 13) SS BOND : angle 1.63184 ( 26) covalent geometry : bond 0.00256 (17028) covalent geometry : angle 0.65523 (23341) Misc. bond : bond 0.00366 ( 3) *********************** 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 311 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 228 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 PHE cc_start: 0.8421 (t80) cc_final: 0.8022 (t80) REVERT: A 642 ILE cc_start: 0.9444 (tp) cc_final: 0.9143 (tp) REVERT: B 153 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9041 (mp) REVERT: B 403 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9052 (pp) REVERT: B 452 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7997 (pp) REVERT: B 628 MET cc_start: 0.7363 (ttt) cc_final: 0.6928 (ttm) REVERT: B 658 ASP cc_start: 0.7517 (m-30) cc_final: 0.6468 (p0) REVERT: C 739 GLU cc_start: 0.8679 (tp30) cc_final: 0.8300 (tp30) REVERT: D 476 TYR cc_start: 0.7272 (t80) cc_final: 0.6954 (t80) REVERT: D 480 ASN cc_start: 0.8327 (t0) cc_final: 0.7916 (t0) REVERT: D 699 MET cc_start: 0.8076 (tpt) cc_final: 0.7494 (mpp) REVERT: D 794 LEU cc_start: 0.8310 (tp) cc_final: 0.8097 (pp) outliers start: 83 outliers final: 59 residues processed: 291 average time/residue: 0.2070 time to fit residues: 100.3982 Evaluate side-chains 277 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 798 CYS Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 76 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 167 optimal weight: 0.0970 chunk 27 optimal weight: 9.9990 chunk 148 optimal weight: 30.0000 overall best weight: 2.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN C 705 HIS D 612 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097308 restraints weight = 40500.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.097795 restraints weight = 27509.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097922 restraints weight = 24971.261| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17060 Z= 0.160 Angle : 0.684 13.138 23415 Z= 0.337 Chirality : 0.045 0.268 2875 Planarity : 0.004 0.063 2951 Dihedral : 7.498 57.031 2810 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.36 % Allowed : 26.03 % Favored : 68.60 % 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: -1.77 (0.17), residues: 2300 helix: 0.58 (0.18), residues: 873 sheet: -1.35 (0.32), residues: 260 loop : -2.63 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 PHE 0.025 0.001 PHE D 635 TYR 0.029 0.001 TYR A 647 ARG 0.002 0.000 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 10) link_NAG-ASN : angle 3.03866 ( 30) link_BETA1-4 : bond 0.00907 ( 6) link_BETA1-4 : angle 2.90529 ( 18) hydrogen bonds : bond 0.03902 ( 637) hydrogen bonds : angle 4.50346 ( 1842) SS BOND : bond 0.00417 ( 13) SS BOND : angle 1.84178 ( 26) covalent geometry : bond 0.00377 (17028) covalent geometry : angle 0.66867 (23341) Misc. bond : bond 0.00356 ( 3) *********************** 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 288 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 205 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 PHE cc_start: 0.8432 (t80) cc_final: 0.8054 (t80) REVERT: A 642 ILE cc_start: 0.9435 (tp) cc_final: 0.9157 (tp) REVERT: B 153 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8857 (mp) REVERT: B 403 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9086 (pp) REVERT: B 452 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8118 (pp) REVERT: B 628 MET cc_start: 0.7373 (ttt) cc_final: 0.6944 (ttm) REVERT: B 658 ASP cc_start: 0.7573 (m-30) cc_final: 0.6475 (p0) REVERT: C 739 GLU cc_start: 0.8731 (tp30) cc_final: 0.8380 (tp30) REVERT: D 476 TYR cc_start: 0.7240 (t80) cc_final: 0.6920 (t80) REVERT: D 480 ASN cc_start: 0.8360 (t0) cc_final: 0.7946 (t0) REVERT: D 699 MET cc_start: 0.8120 (tpt) cc_final: 0.7475 (mpp) REVERT: D 736 MET cc_start: 0.8571 (tpp) cc_final: 0.8117 (ttm) REVERT: D 794 LEU cc_start: 0.8280 (tp) cc_final: 0.8076 (pp) outliers start: 83 outliers final: 72 residues processed: 271 average time/residue: 0.2020 time to fit residues: 92.1764 Evaluate side-chains 281 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 798 CYS Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 228 optimal weight: 0.2980 chunk 2 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3660 r_free = 0.3660 target = 0.122280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.096961 restraints weight = 40875.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097667 restraints weight = 27666.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097926 restraints weight = 23375.721| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17060 Z= 0.151 Angle : 0.685 13.358 23415 Z= 0.337 Chirality : 0.045 0.266 2875 Planarity : 0.004 0.068 2951 Dihedral : 7.455 57.042 2810 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 5.49 % Allowed : 26.03 % Favored : 68.48 % 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: -1.75 (0.17), residues: 2300 helix: 0.60 (0.18), residues: 871 sheet: -1.34 (0.32), residues: 260 loop : -2.62 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 PHE 0.024 0.001 PHE D 635 TYR 0.024 0.001 TYR A 647 ARG 0.003 0.000 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 10) link_NAG-ASN : angle 3.03276 ( 30) link_BETA1-4 : bond 0.00974 ( 6) link_BETA1-4 : angle 2.89142 ( 18) hydrogen bonds : bond 0.03862 ( 637) hydrogen bonds : angle 4.47835 ( 1842) SS BOND : bond 0.00420 ( 13) SS BOND : angle 1.76355 ( 26) covalent geometry : bond 0.00356 (17028) covalent geometry : angle 0.66960 (23341) Misc. bond : bond 0.00356 ( 3) *********************** 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 295 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 PHE cc_start: 0.8464 (t80) cc_final: 0.8083 (t80) REVERT: A 642 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9137 (tp) REVERT: B 150 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8509 (mp) REVERT: B 153 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8837 (mp) REVERT: B 403 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9078 (pp) REVERT: B 452 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8086 (pp) REVERT: B 628 MET cc_start: 0.7361 (ttt) cc_final: 0.6942 (ttm) REVERT: B 658 ASP cc_start: 0.7552 (m-30) cc_final: 0.6461 (p0) REVERT: C 739 GLU cc_start: 0.8740 (tp30) cc_final: 0.8391 (tp30) REVERT: D 476 TYR cc_start: 0.7289 (t80) cc_final: 0.6961 (t80) REVERT: D 480 ASN cc_start: 0.8550 (t0) cc_final: 0.8204 (t0) REVERT: D 699 MET cc_start: 0.8144 (tpt) cc_final: 0.7476 (mpp) REVERT: D 736 MET cc_start: 0.8640 (tpp) cc_final: 0.8171 (ttm) REVERT: D 794 LEU cc_start: 0.8305 (tp) cc_final: 0.8068 (pp) outliers start: 85 outliers final: 70 residues processed: 274 average time/residue: 0.2050 time to fit residues: 94.0556 Evaluate side-chains 279 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 204 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 798 CYS Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097150 restraints weight = 40545.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096061 restraints weight = 30733.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097013 restraints weight = 25248.772| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17060 Z= 0.170 Angle : 0.703 13.534 23415 Z= 0.346 Chirality : 0.045 0.275 2875 Planarity : 0.004 0.065 2951 Dihedral : 7.500 57.635 2810 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 5.49 % Allowed : 26.36 % Favored : 68.15 % 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: -1.78 (0.17), residues: 2300 helix: 0.58 (0.18), residues: 872 sheet: -1.38 (0.32), residues: 260 loop : -2.64 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 PHE 0.031 0.001 PHE D 635 TYR 0.023 0.001 TYR C 681 ARG 0.004 0.000 ARG C 671 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 10) link_NAG-ASN : angle 3.06932 ( 30) link_BETA1-4 : bond 0.00957 ( 6) link_BETA1-4 : angle 2.87984 ( 18) hydrogen bonds : bond 0.03978 ( 637) hydrogen bonds : angle 4.51039 ( 1842) SS BOND : bond 0.00431 ( 13) SS BOND : angle 1.84003 ( 26) covalent geometry : bond 0.00402 (17028) covalent geometry : angle 0.68832 (23341) Misc. bond : bond 0.00356 ( 3) ********************** 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 291 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 206 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 PHE cc_start: 0.8561 (t80) cc_final: 0.8147 (t80) REVERT: A 641 MET cc_start: 0.8894 (tpp) cc_final: 0.8631 (tpp) REVERT: A 642 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9103 (tp) REVERT: B 150 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 153 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8838 (mp) REVERT: B 403 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9098 (pp) REVERT: B 452 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8102 (pp) REVERT: B 628 MET cc_start: 0.7355 (ttt) cc_final: 0.6945 (ttm) REVERT: B 658 ASP cc_start: 0.7651 (m-30) cc_final: 0.6459 (p0) REVERT: C 739 GLU cc_start: 0.8767 (tp30) cc_final: 0.8414 (tp30) REVERT: D 476 TYR cc_start: 0.7399 (t80) cc_final: 0.7078 (t80) REVERT: D 480 ASN cc_start: 0.8654 (t0) cc_final: 0.8310 (t0) REVERT: D 549 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 699 MET cc_start: 0.8204 (tpt) cc_final: 0.7515 (mpp) REVERT: D 794 LEU cc_start: 0.8384 (tp) cc_final: 0.8092 (pp) outliers start: 85 outliers final: 76 residues processed: 271 average time/residue: 0.1975 time to fit residues: 90.1729 Evaluate side-chains 285 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 204 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 612 ASN Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 798 CYS Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 106 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 167 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3657 r_free = 0.3657 target = 0.122035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097350 restraints weight = 40621.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096316 restraints weight = 30890.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097263 restraints weight = 25127.835| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17060 Z= 0.172 Angle : 0.965 59.199 23415 Z= 0.548 Chirality : 0.045 0.434 2875 Planarity : 0.005 0.065 2951 Dihedral : 7.510 57.589 2810 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.04 % Favored : 89.91 % Rotamer: Outliers : 5.75 % Allowed : 25.97 % Favored : 68.28 % Cbeta Deviations : 0.09 % 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: -1.75 (0.17), residues: 2300 helix: 0.61 (0.18), residues: 870 sheet: -1.38 (0.32), residues: 260 loop : -2.62 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 PHE 0.025 0.001 PHE D 635 TYR 0.021 0.001 TYR C 681 ARG 0.004 0.000 ARG C 671 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 10) link_NAG-ASN : angle 3.06154 ( 30) link_BETA1-4 : bond 0.00954 ( 6) link_BETA1-4 : angle 2.91812 ( 18) hydrogen bonds : bond 0.04007 ( 637) hydrogen bonds : angle 4.52254 ( 1842) SS BOND : bond 0.00457 ( 13) SS BOND : angle 1.77161 ( 26) covalent geometry : bond 0.00369 (17028) covalent geometry : angle 0.95521 (23341) Misc. bond : bond 0.00368 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5323.74 seconds wall clock time: 93 minutes 56.12 seconds (5636.12 seconds total)