Starting phenix.real_space_refine on Thu Feb 5 10:20:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e93_27954/02_2026/8e93_27954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e93_27954/02_2026/8e93_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e93_27954/02_2026/8e93_27954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e93_27954/02_2026/8e93_27954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e93_27954/02_2026/8e93_27954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e93_27954/02_2026/8e93_27954.map" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'ARG:plan': 20, 'GLU:plan': 39, 'GLN:plan1': 10, 'ASN:plan1': 12, 'HIS:plan': 4, 'TRP:plan': 2, 'PHE:plan': 7, 'ASP:plan': 17, 'TYR:plan': 3} 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, 'PHE:plan': 4, 'ARG:plan': 12, 'ASP:plan': 8, 'GLU:plan': 15, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2} 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: {'GLU:plan': 10, 'ASP:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'PHE:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2} 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: {'ARG:plan': 17, 'HIS:plan': 4, 'GLU:plan': 16, 'ASP:plan': 7, 'GLN:plan1': 10, 'ASN:plan1': 4, 'PHE:plan': 10, 'TYR:plan': 9, 'TRP:plan': 2} 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: 3.60, per 1000 atoms: 0.22 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: 1.35 Conformation dependent library (CDL) restraints added in 654.2 milliseconds 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: 0.62 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: 2.78 Time building geometry restraints manager: 1.79 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: 5.840 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.190 ------------------------------------------------------------------------------- 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 : 8.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG B 389 TYR 0.058 0.001 TYR B 390 PHE 0.022 0.001 PHE C 654 TRP 0.020 0.001 TRP D 632 HIS 0.017 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00452 (17028) covalent geometry : angle 0.83428 (23341) SS BOND : bond 0.00412 ( 13) SS BOND : angle 1.72133 ( 26) hydrogen bonds : bond 0.31071 ( 637) hydrogen bonds : angle 8.69785 ( 1842) Misc. bond : bond 0.00517 ( 3) link_BETA1-4 : bond 0.01498 ( 6) link_BETA1-4 : angle 3.00948 ( 18) link_NAG-ASN : bond 0.00768 ( 10) link_NAG-ASN : angle 3.89199 ( 30) *********************** 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 : 0.626 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: 0.7694 (t0) outliers start: 10 outliers final: 6 residues processed: 242 average time/residue: 0.0897 time to fit residues: 36.7147 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 : 0.602 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.118813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094727 restraints weight = 40539.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094988 restraints weight = 26716.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095358 restraints weight = 26438.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095821 restraints weight = 20165.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096213 restraints weight = 18265.416| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 17060 Z= 0.280 Angle : 0.821 11.639 23415 Z= 0.417 Chirality : 0.050 0.333 2875 Planarity : 0.006 0.111 2951 Dihedral : 10.451 85.004 2818 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.30 % Favored : 88.65 % Rotamer: Outliers : 7.30 % Allowed : 21.19 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.16), residues: 2300 helix: -0.37 (0.17), residues: 866 sheet: -1.89 (0.32), residues: 249 loop : -2.86 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 389 TYR 0.019 0.002 TYR C 681 PHE 0.023 0.002 PHE B 526 TRP 0.018 0.002 TRP C 792 HIS 0.014 0.002 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00649 (17028) covalent geometry : angle 0.80437 (23341) SS BOND : bond 0.00483 ( 13) SS BOND : angle 2.45058 ( 26) hydrogen bonds : bond 0.06404 ( 637) hydrogen bonds : angle 5.80698 ( 1842) Misc. bond : bond 0.00423 ( 3) link_BETA1-4 : bond 0.00941 ( 6) link_BETA1-4 : angle 2.82289 ( 18) link_NAG-ASN : bond 0.00479 ( 10) link_NAG-ASN : angle 3.53821 ( 30) *********************** 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 336 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 223 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8392 (pp) REVERT: A 125 MET cc_start: 0.8644 (mmm) cc_final: 0.7026 (mmm) REVERT: A 180 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 545 GLU cc_start: 0.7553 (pm20) cc_final: 0.7311 (pm20) REVERT: B 153 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8845 (mp) REVERT: B 403 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9010 (pp) REVERT: B 452 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8277 (pp) REVERT: C 690 ASP cc_start: 0.9135 (t70) cc_final: 0.8829 (t0) REVERT: C 739 GLU cc_start: 0.8770 (tp30) cc_final: 0.8238 (tp30) REVERT: D 696 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: D 794 LEU cc_start: 0.8431 (tp) cc_final: 0.8089 (pp) outliers start: 113 outliers final: 75 residues processed: 313 average time/residue: 0.0922 time to fit residues: 48.6891 Evaluate side-chains 290 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 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 411 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 130 LEU 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 201 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 276 VAL 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 397 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 462 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 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 786 THR 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 539 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR 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 752 LEU Chi-restraints excluded: chain C residue 781 GLU 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 570 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 676 PRO Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 696 TYR Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 822 LEU 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 173 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 224 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 171 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095531 restraints weight = 40925.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095799 restraints weight = 26478.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096428 restraints weight = 26807.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096634 restraints weight = 20289.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096970 restraints weight = 18233.922| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17060 Z= 0.208 Angle : 0.743 11.854 23415 Z= 0.375 Chirality : 0.047 0.320 2875 Planarity : 0.005 0.082 2951 Dihedral : 9.336 78.552 2815 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.26 % Favored : 89.70 % Rotamer: Outliers : 6.98 % Allowed : 22.35 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.17), residues: 2300 helix: -0.14 (0.17), residues: 866 sheet: -1.74 (0.32), residues: 246 loop : -2.85 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 671 TYR 0.016 0.001 TYR B 449 PHE 0.021 0.002 PHE D 635 TRP 0.018 0.001 TRP C 792 HIS 0.015 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00482 (17028) covalent geometry : angle 0.72586 (23341) SS BOND : bond 0.00624 ( 13) SS BOND : angle 2.04098 ( 26) hydrogen bonds : bond 0.05557 ( 637) hydrogen bonds : angle 5.31583 ( 1842) Misc. bond : bond 0.00386 ( 3) link_BETA1-4 : bond 0.01063 ( 6) link_BETA1-4 : angle 3.04115 ( 18) link_NAG-ASN : bond 0.00451 ( 10) link_NAG-ASN : angle 3.36965 ( 30) *********************** 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 338 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 230 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 455 CYS cc_start: 0.5096 (m) cc_final: 0.4849 (m) REVERT: A 545 GLU cc_start: 0.7607 (pm20) cc_final: 0.7293 (pm20) REVERT: A 639 PHE cc_start: 0.8397 (t80) cc_final: 0.8011 (t80) REVERT: B 153 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8858 (mp) REVERT: B 403 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9029 (pp) REVERT: B 452 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8146 (pp) REVERT: C 690 ASP cc_start: 0.9073 (t70) cc_final: 0.8847 (t0) REVERT: C 739 GLU cc_start: 0.8762 (tp30) cc_final: 0.8313 (tp30) REVERT: C 787 ASP cc_start: 0.8095 (p0) cc_final: 0.7858 (p0) REVERT: D 480 ASN cc_start: 0.8414 (t0) cc_final: 0.7962 (t0) REVERT: D 513 ASN cc_start: 0.7221 (p0) cc_final: 0.6972 (p0) REVERT: D 794 LEU cc_start: 0.8446 (tp) cc_final: 0.8124 (pp) outliers start: 108 outliers final: 73 residues processed: 311 average time/residue: 0.0839 time to fit residues: 44.8210 Evaluate side-chains 285 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 208 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 198 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 748 THR 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 90 VAL Chi-restraints excluded: chain B residue 97 ASP 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 201 LEU 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 359 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR 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 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 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 539 THR 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 741 SER Chi-restraints excluded: chain C residue 744 CYS 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 676 PRO 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 36 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095207 restraints weight = 40503.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094496 restraints weight = 26712.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095142 restraints weight = 24515.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095436 restraints weight = 19668.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095921 restraints weight = 18208.174| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1879 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= 0.187 Angle : 0.721 13.327 23415 Z= 0.361 Chirality : 0.046 0.265 2875 Planarity : 0.005 0.072 2951 Dihedral : 8.651 73.537 2810 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.61 % Favored : 89.35 % Rotamer: Outliers : 8.01 % Allowed : 22.48 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2300 helix: 0.01 (0.17), residues: 869 sheet: -1.97 (0.31), residues: 264 loop : -2.81 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 389 TYR 0.015 0.001 TYR B 476 PHE 0.020 0.001 PHE D 635 TRP 0.018 0.001 TRP C 792 HIS 0.015 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00436 (17028) covalent geometry : angle 0.70557 (23341) SS BOND : bond 0.00682 ( 13) SS BOND : angle 1.68671 ( 26) hydrogen bonds : bond 0.04838 ( 637) hydrogen bonds : angle 5.03164 ( 1842) Misc. bond : bond 0.00381 ( 3) link_BETA1-4 : bond 0.00892 ( 6) link_BETA1-4 : angle 3.03703 ( 18) link_NAG-ASN : bond 0.00392 ( 10) link_NAG-ASN : angle 3.24405 ( 30) *********************** 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 339 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 215 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8400 (pp) REVERT: A 180 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8414 (tt) REVERT: A 455 CYS cc_start: 0.5432 (m) cc_final: 0.5191 (m) REVERT: A 545 GLU cc_start: 0.7572 (pm20) cc_final: 0.7207 (pm20) REVERT: A 639 PHE cc_start: 0.8565 (t80) cc_final: 0.8164 (t80) REVERT: A 642 ILE cc_start: 0.9520 (tp) cc_final: 0.9174 (tp) REVERT: B 153 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8834 (mp) REVERT: B 403 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9092 (pp) REVERT: B 452 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8027 (pp) REVERT: C 672 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8292 (mm) REVERT: C 739 GLU cc_start: 0.8796 (tp30) cc_final: 0.8396 (tp30) REVERT: D 476 TYR cc_start: 0.7171 (t80) cc_final: 0.6963 (t80) REVERT: D 480 ASN cc_start: 0.8569 (t0) cc_final: 0.8149 (t0) REVERT: D 696 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5996 (m-10) REVERT: D 794 LEU cc_start: 0.8541 (tp) cc_final: 0.8197 (pp) outliers start: 124 outliers final: 86 residues processed: 311 average time/residue: 0.0851 time to fit residues: 45.2432 Evaluate side-chains 297 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 204 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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 542 VAL 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 683 THR Chi-restraints excluded: chain A residue 687 SER 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 66 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 ASP 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 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 291 ASP 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 359 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 450 THR 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 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 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 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 490 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 672 LEU 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 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 609 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 676 PRO 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 786 THR Chi-restraints excluded: chain D residue 798 CYS Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 822 LEU 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 130 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN B 672 GLN D 612 ASN ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096534 restraints weight = 40317.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095770 restraints weight = 27516.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096494 restraints weight = 23583.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096889 restraints weight = 19062.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097100 restraints weight = 17581.286| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17060 Z= 0.159 Angle : 0.697 12.719 23415 Z= 0.347 Chirality : 0.045 0.260 2875 Planarity : 0.004 0.070 2951 Dihedral : 8.265 68.051 2810 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.78 % Favored : 90.17 % Rotamer: Outliers : 7.88 % Allowed : 22.48 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.17), residues: 2300 helix: 0.19 (0.18), residues: 868 sheet: -1.67 (0.32), residues: 252 loop : -2.78 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 389 TYR 0.014 0.001 TYR B 476 PHE 0.022 0.001 PHE D 635 TRP 0.017 0.001 TRP C 792 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00369 (17028) covalent geometry : angle 0.68117 (23341) SS BOND : bond 0.00426 ( 13) SS BOND : angle 1.73479 ( 26) hydrogen bonds : bond 0.04397 ( 637) hydrogen bonds : angle 4.80307 ( 1842) Misc. bond : bond 0.00374 ( 3) link_BETA1-4 : bond 0.00981 ( 6) link_BETA1-4 : angle 2.95506 ( 18) link_NAG-ASN : bond 0.00416 ( 10) link_NAG-ASN : angle 3.12839 ( 30) *********************** 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 338 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 216 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8327 (pp) REVERT: A 180 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 455 CYS cc_start: 0.5398 (m) cc_final: 0.5140 (m) REVERT: A 545 GLU cc_start: 0.7580 (pm20) cc_final: 0.7172 (pm20) REVERT: A 639 PHE cc_start: 0.8544 (t80) cc_final: 0.8141 (t80) REVERT: A 642 ILE cc_start: 0.9504 (tp) cc_final: 0.9120 (tp) REVERT: B 153 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 403 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9084 (pp) REVERT: B 452 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8049 (pp) REVERT: B 462 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8590 (tp) REVERT: C 672 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8293 (mm) REVERT: C 739 GLU cc_start: 0.8773 (tp30) cc_final: 0.8408 (tp30) REVERT: D 480 ASN cc_start: 0.8478 (t0) cc_final: 0.8086 (t0) REVERT: D 696 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.5931 (m-10) REVERT: D 794 LEU cc_start: 0.8498 (tp) cc_final: 0.8180 (pp) outliers start: 122 outliers final: 88 residues processed: 307 average time/residue: 0.0801 time to fit residues: 42.4219 Evaluate side-chains 301 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 205 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 542 VAL 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 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 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 90 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 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 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 372 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 462 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 631 VAL 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 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 451 VAL Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 672 LEU 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 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 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 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 696 TYR 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 822 LEU 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 115 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.0010 chunk 148 optimal weight: 30.0000 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.122946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097815 restraints weight = 40297.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097651 restraints weight = 28384.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098198 restraints weight = 24622.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098591 restraints weight = 19946.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098766 restraints weight = 18422.651| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2202 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= 0.124 Angle : 0.680 13.162 23415 Z= 0.337 Chirality : 0.045 0.309 2875 Planarity : 0.004 0.067 2951 Dihedral : 7.798 58.396 2810 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 6.01 % Allowed : 24.81 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.17), residues: 2300 helix: 0.37 (0.18), residues: 877 sheet: -1.49 (0.33), residues: 245 loop : -2.67 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 389 TYR 0.017 0.001 TYR C 681 PHE 0.027 0.001 PHE D 635 TRP 0.022 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00277 (17028) covalent geometry : angle 0.66313 (23341) SS BOND : bond 0.00567 ( 13) SS BOND : angle 2.13673 ( 26) hydrogen bonds : bond 0.03862 ( 637) hydrogen bonds : angle 4.60006 ( 1842) Misc. bond : bond 0.00365 ( 3) link_BETA1-4 : bond 0.00997 ( 6) link_BETA1-4 : angle 2.91220 ( 18) link_NAG-ASN : bond 0.00536 ( 10) link_NAG-ASN : angle 3.14379 ( 30) *********************** 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 315 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 222 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5318 (m) cc_final: 0.5059 (m) REVERT: A 639 PHE cc_start: 0.8426 (t80) cc_final: 0.8048 (t80) REVERT: A 642 ILE cc_start: 0.9496 (tp) cc_final: 0.9124 (tp) REVERT: A 744 CYS cc_start: 0.4398 (OUTLIER) cc_final: 0.3247 (t) REVERT: B 153 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9097 (mp) REVERT: B 403 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9029 (pp) REVERT: B 452 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7986 (pp) REVERT: B 658 ASP cc_start: 0.7608 (m-30) cc_final: 0.6497 (p0) REVERT: C 672 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8354 (mm) REVERT: C 739 GLU cc_start: 0.8699 (tp30) cc_final: 0.8338 (tp30) REVERT: D 480 ASN cc_start: 0.8321 (t0) cc_final: 0.7923 (t0) REVERT: D 699 MET cc_start: 0.7850 (tpt) cc_final: 0.7400 (mpp) REVERT: D 794 LEU cc_start: 0.8370 (tp) cc_final: 0.8138 (pp) outliers start: 93 outliers final: 62 residues processed: 292 average time/residue: 0.0829 time to fit residues: 41.1646 Evaluate side-chains 275 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 208 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 118 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 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 635 VAL Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 752 LEU 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 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 153 LEU 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 298 LEU Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 403 LEU 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 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 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 451 VAL Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 672 LEU 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 627 ILE Chi-restraints excluded: chain D residue 657 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 172 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 206 optimal weight: 0.0970 chunk 120 optimal weight: 0.0670 chunk 188 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.1920 ------------------------------------------------------------------------------- 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 D 612 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098368 restraints weight = 40567.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097981 restraints weight = 28529.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098492 restraints weight = 25876.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098840 restraints weight = 21304.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099052 restraints weight = 18910.916| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17060 Z= 0.125 Angle : 0.670 11.631 23415 Z= 0.329 Chirality : 0.044 0.280 2875 Planarity : 0.004 0.063 2951 Dihedral : 7.528 56.124 2810 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 6.27 % Allowed : 25.39 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.17), residues: 2300 helix: 0.52 (0.18), residues: 875 sheet: -1.43 (0.32), residues: 245 loop : -2.64 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 763 TYR 0.020 0.001 TYR B 476 PHE 0.025 0.001 PHE D 635 TRP 0.022 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00287 (17028) covalent geometry : angle 0.65424 (23341) SS BOND : bond 0.00412 ( 13) SS BOND : angle 1.93861 ( 26) hydrogen bonds : bond 0.03685 ( 637) hydrogen bonds : angle 4.43576 ( 1842) Misc. bond : bond 0.00358 ( 3) link_BETA1-4 : bond 0.00988 ( 6) link_BETA1-4 : angle 2.93042 ( 18) link_NAG-ASN : bond 0.00499 ( 10) link_NAG-ASN : angle 3.01293 ( 30) *********************** 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 317 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 220 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5306 (m) cc_final: 0.5050 (m) REVERT: A 639 PHE cc_start: 0.8412 (t80) cc_final: 0.8037 (t80) REVERT: A 642 ILE cc_start: 0.9454 (tp) cc_final: 0.9167 (tp) REVERT: B 153 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8904 (mp) REVERT: B 403 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9008 (pp) REVERT: B 452 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8010 (pp) REVERT: B 628 MET cc_start: 0.7433 (ttt) cc_final: 0.6987 (ttm) REVERT: B 658 ASP cc_start: 0.7606 (m-30) cc_final: 0.6523 (p0) REVERT: C 672 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (mm) REVERT: C 739 GLU cc_start: 0.8680 (tp30) cc_final: 0.8366 (tp30) REVERT: C 780 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8399 (t-90) REVERT: D 480 ASN cc_start: 0.8331 (t0) cc_final: 0.7911 (t0) REVERT: D 699 MET cc_start: 0.7873 (tpt) cc_final: 0.7423 (mpp) REVERT: D 794 LEU cc_start: 0.8331 (tp) cc_final: 0.8093 (pp) outliers start: 97 outliers final: 72 residues processed: 297 average time/residue: 0.0845 time to fit residues: 42.3549 Evaluate side-chains 283 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 206 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 LEU 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 635 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 744 CYS 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 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 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 629 VAL 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 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 634 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 672 LEU 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 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 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 34 optimal weight: 0.0040 chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 overall best weight: 4.2998 ------------------------------------------------------------------------------- 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 C 650 ASN D 612 ASN ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094400 restraints weight = 40924.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.094500 restraints weight = 27885.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094954 restraints weight = 26997.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095474 restraints weight = 21412.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095742 restraints weight = 19403.087| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 17060 Z= 0.261 Angle : 0.782 10.393 23415 Z= 0.391 Chirality : 0.048 0.276 2875 Planarity : 0.005 0.064 2951 Dihedral : 8.073 59.519 2810 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 7.04 % Allowed : 25.26 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 2300 helix: 0.29 (0.17), residues: 870 sheet: -1.81 (0.32), residues: 256 loop : -2.75 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.033 0.002 TYR A 647 PHE 0.026 0.002 PHE D 635 TRP 0.024 0.002 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00614 (17028) covalent geometry : angle 0.76603 (23341) SS BOND : bond 0.00587 ( 13) SS BOND : angle 2.28126 ( 26) hydrogen bonds : bond 0.04774 ( 637) hydrogen bonds : angle 4.87981 ( 1842) Misc. bond : bond 0.00367 ( 3) link_BETA1-4 : bond 0.00969 ( 6) link_BETA1-4 : angle 2.85439 ( 18) link_NAG-ASN : bond 0.00458 ( 10) link_NAG-ASN : angle 3.37707 ( 30) *********************** 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 319 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 210 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5361 (m) cc_final: 0.5153 (m) REVERT: A 639 PHE cc_start: 0.8469 (t80) cc_final: 0.8069 (t80) REVERT: A 642 ILE cc_start: 0.9503 (tp) cc_final: 0.9192 (tp) REVERT: B 153 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8846 (mp) REVERT: B 403 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9058 (pp) REVERT: B 452 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8250 (pp) REVERT: B 658 ASP cc_start: 0.7855 (m-30) cc_final: 0.6616 (p0) REVERT: D 480 ASN cc_start: 0.8379 (t0) cc_final: 0.7973 (t0) REVERT: D 549 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 556 TRP cc_start: 0.8431 (m100) cc_final: 0.8136 (m100) REVERT: D 696 TYR cc_start: 0.6527 (OUTLIER) cc_final: 0.6177 (m-10) REVERT: D 794 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8076 (pp) outliers start: 109 outliers final: 90 residues processed: 297 average time/residue: 0.0914 time to fit residues: 46.2446 Evaluate side-chains 299 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 204 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 107 VAL 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 180 LEU 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 478 LEU Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 542 VAL 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 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 97 ASP 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 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 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 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 479 VAL Chi-restraints excluded: chain C residue 568 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 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 527 VAL 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 696 TYR Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 814 ASN Chi-restraints excluded: chain D residue 822 LEU 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 85 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 D 612 ASN ** D 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097318 restraints weight = 40329.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096775 restraints weight = 29911.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097323 restraints weight = 25614.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097793 restraints weight = 21035.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097939 restraints weight = 19108.297| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17060 Z= 0.131 Angle : 0.703 12.275 23415 Z= 0.342 Chirality : 0.045 0.374 2875 Planarity : 0.004 0.063 2951 Dihedral : 7.651 56.584 2810 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 5.81 % Allowed : 26.49 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 2300 helix: 0.50 (0.17), residues: 875 sheet: -1.46 (0.33), residues: 246 loop : -2.64 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 763 TYR 0.018 0.001 TYR A 647 PHE 0.022 0.001 PHE D 635 TRP 0.019 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00303 (17028) covalent geometry : angle 0.68662 (23341) SS BOND : bond 0.00425 ( 13) SS BOND : angle 1.69873 ( 26) hydrogen bonds : bond 0.03779 ( 637) hydrogen bonds : angle 4.48613 ( 1842) Misc. bond : bond 0.00364 ( 3) link_BETA1-4 : bond 0.00994 ( 6) link_BETA1-4 : angle 2.85989 ( 18) link_NAG-ASN : bond 0.00439 ( 10) link_NAG-ASN : angle 3.33229 ( 30) *********************** 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 306 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 216 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5491 (m) cc_final: 0.5222 (m) REVERT: A 545 GLU cc_start: 0.7523 (pm20) cc_final: 0.7301 (pm20) REVERT: A 639 PHE cc_start: 0.8463 (t80) cc_final: 0.8075 (t80) REVERT: A 641 MET cc_start: 0.8840 (tpp) cc_final: 0.8604 (tpp) REVERT: A 642 ILE cc_start: 0.9408 (tp) cc_final: 0.9118 (tp) REVERT: B 153 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9055 (mp) REVERT: B 403 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9036 (pp) REVERT: B 452 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8123 (pp) REVERT: B 628 MET cc_start: 0.7429 (ttt) cc_final: 0.6966 (ttm) REVERT: B 658 ASP cc_start: 0.7707 (m-30) cc_final: 0.6512 (p0) REVERT: B 661 SER cc_start: 0.9299 (m) cc_final: 0.8809 (t) REVERT: D 480 ASN cc_start: 0.8388 (t0) cc_final: 0.7967 (t0) REVERT: D 556 TRP cc_start: 0.8316 (m100) cc_final: 0.8070 (m100) REVERT: D 699 MET cc_start: 0.8045 (tpt) cc_final: 0.7491 (mpp) REVERT: D 736 MET cc_start: 0.8436 (ttp) cc_final: 0.8179 (ttm) REVERT: D 794 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8101 (pp) outliers start: 90 outliers final: 79 residues processed: 285 average time/residue: 0.1006 time to fit residues: 48.5849 Evaluate side-chains 291 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 208 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 118 VAL 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 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 296 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 542 VAL 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 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 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 339 THR 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 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 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 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 568 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 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 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 756 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 794 LEU 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 179 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 D 612 ASN D 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098029 restraints weight = 40464.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.097769 restraints weight = 31017.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098157 restraints weight = 26479.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098606 restraints weight = 21323.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098802 restraints weight = 19279.861| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2596 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= 0.122 Angle : 0.697 11.356 23415 Z= 0.338 Chirality : 0.045 0.364 2875 Planarity : 0.004 0.064 2951 Dihedral : 7.440 56.192 2810 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 5.30 % Allowed : 27.13 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2300 helix: 0.59 (0.18), residues: 874 sheet: -1.37 (0.32), residues: 260 loop : -2.62 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.021 0.001 TYR C 681 PHE 0.025 0.001 PHE D 635 TRP 0.021 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00280 (17028) covalent geometry : angle 0.68128 (23341) SS BOND : bond 0.00414 ( 13) SS BOND : angle 1.56710 ( 26) hydrogen bonds : bond 0.03586 ( 637) hydrogen bonds : angle 4.37797 ( 1842) Misc. bond : bond 0.00361 ( 3) link_BETA1-4 : bond 0.01020 ( 6) link_BETA1-4 : angle 2.93083 ( 18) link_NAG-ASN : bond 0.00646 ( 10) link_NAG-ASN : angle 3.31696 ( 30) ********************** 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 296 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 214 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5376 (m) cc_final: 0.5092 (m) REVERT: A 639 PHE cc_start: 0.8419 (t80) cc_final: 0.8041 (t80) REVERT: A 641 MET cc_start: 0.8806 (tpp) cc_final: 0.8565 (tpp) REVERT: A 642 ILE cc_start: 0.9339 (tp) cc_final: 0.9079 (tp) REVERT: B 153 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9050 (mp) REVERT: B 403 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9044 (pp) REVERT: B 452 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8109 (pp) REVERT: B 628 MET cc_start: 0.7363 (ttt) cc_final: 0.6924 (ttm) REVERT: B 658 ASP cc_start: 0.7620 (m-30) cc_final: 0.6511 (p0) REVERT: C 739 GLU cc_start: 0.8705 (tp30) cc_final: 0.8406 (tp30) REVERT: D 480 ASN cc_start: 0.8551 (t0) cc_final: 0.8180 (t0) REVERT: D 556 TRP cc_start: 0.8321 (m100) cc_final: 0.8070 (m100) REVERT: D 699 MET cc_start: 0.8018 (tpt) cc_final: 0.7489 (mpp) REVERT: D 736 MET cc_start: 0.8378 (ttp) cc_final: 0.8141 (ttp) REVERT: D 794 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8096 (pp) outliers start: 82 outliers final: 73 residues processed: 275 average time/residue: 0.0997 time to fit residues: 46.5439 Evaluate side-chains 286 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 118 VAL 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 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 542 VAL 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 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 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 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 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 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 472 PHE Chi-restraints excluded: chain C residue 568 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 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 507 ILE Chi-restraints excluded: chain D residue 509 SER 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 756 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 794 LEU 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 161 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 102 optimal weight: 0.0010 chunk 94 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.123004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098404 restraints weight = 40260.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098358 restraints weight = 29673.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098884 restraints weight = 25856.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099272 restraints weight = 20041.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099417 restraints weight = 18439.263| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17060 Z= 0.134 Angle : 0.694 11.114 23415 Z= 0.338 Chirality : 0.045 0.349 2875 Planarity : 0.004 0.061 2951 Dihedral : 7.337 56.252 2810 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.68 % Allowed : 26.68 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.17), residues: 2300 helix: 0.64 (0.18), residues: 876 sheet: -1.30 (0.32), residues: 260 loop : -2.58 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 671 TYR 0.023 0.001 TYR C 681 PHE 0.025 0.001 PHE D 635 TRP 0.020 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00312 (17028) covalent geometry : angle 0.67836 (23341) SS BOND : bond 0.00381 ( 13) SS BOND : angle 1.59490 ( 26) hydrogen bonds : bond 0.03591 ( 637) hydrogen bonds : angle 4.36805 ( 1842) Misc. bond : bond 0.00355 ( 3) link_BETA1-4 : bond 0.00967 ( 6) link_BETA1-4 : angle 2.88937 ( 18) link_NAG-ASN : bond 0.00590 ( 10) link_NAG-ASN : angle 3.29454 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2687.63 seconds wall clock time: 47 minutes 4.85 seconds (2824.85 seconds total)