Starting phenix.real_space_refine on Fri Jul 3 23:22:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e93_27954/07_2026/8e93_27954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e93_27954/07_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_27954/07_2026/8e93_27954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e93_27954/07_2026/8e93_27954.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8e93_27954/07_2026/8e93_27954.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e93_27954/07_2026/8e93_27954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e93_27954/07_2026/8e93_27954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e93_27954/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.41, per 1000 atoms: 0.20 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: 1.42 Conformation dependent library (CDL) restraints added in 798.7 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: 0.37 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: 2.83 Time building geometry restraints manager: 1.87 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 - 17.31: 8702 17.31 - 34.62: 859 34.62 - 51.93: 223 51.93 - 69.24: 27 69.24 - 86.56: 17 Dihedral angle restraints: 9828 sinusoidal: 3141 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 9825 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 15.167 85.060 5471 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/Z covalent geometry : bond 0.00452 / 0.26 (17028) covalent geometry : angle 0.83428 / 0.47 (23341) SS BOND : bond 0.00412 / 0.30 ( 13) SS BOND : angle 1.72133 / 1.22 ( 26) hydrogen bonds : bond 0.31071 / 21.63 ( 637) hydrogen bonds : angle 8.69785 / 6.20 ( 1842) Misc. bond : bond 0.00517 / 0.26 ( 3) link_BETA1-4 : bond 0.01498 / 0.96 ( 6) link_BETA1-4 : angle 3.00948 / 1.82 ( 18) link_NAG-ASN : bond 0.00768 / 0.51 ( 10) link_NAG-ASN : angle 3.89199 / 2.79 ( 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 : 0.756 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: 0.0915 time to fit residues: 37.5748 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 : 0.638 ------------------------------------------------------------------------------- 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... A 453 GLN B 395 GLN D 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094757 restraints weight = 40403.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094732 restraints weight = 27397.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095003 restraints weight = 25639.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096348 restraints weight = 20725.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096332 restraints weight = 16847.698| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17060 Z= 0.271 Angle : 0.797 11.328 23415 Z= 0.408 Chirality : 0.049 0.347 2875 Planarity : 0.006 0.114 2951 Dihedral : 6.501 58.899 2444 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.26 % Favored : 88.70 % Rotamer: Outliers : 6.91 % Allowed : 21.38 % Favored : 71.71 % 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: -0.38 (0.17), residues: 867 sheet: -1.85 (0.32), residues: 254 loop : -2.88 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 389 TYR 0.018 0.002 TYR B 476 PHE 0.023 0.002 PHE B 526 TRP 0.017 0.002 TRP C 792 HIS 0.014 0.002 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 (17028) covalent geometry : angle 0.78269 / 0.40 (23341) SS BOND : bond 0.00695 / 0.54 ( 13) SS BOND : angle 2.39097 / 1.70 ( 26) hydrogen bonds : bond 0.07213 / 4.94 ( 637) hydrogen bonds : angle 5.88348 / 4.19 ( 1842) Misc. bond : bond 0.00424 / 0.21 ( 3) link_BETA1-4 : bond 0.00966 / 0.56 ( 6) link_BETA1-4 : angle 2.11129 / 1.23 ( 18) link_NAG-ASN : bond 0.00518 / 0.33 ( 10) link_NAG-ASN : angle 3.46250 / 2.59 ( 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 326 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 219 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8363 (pp) REVERT: A 125 MET cc_start: 0.8651 (mmm) cc_final: 0.7065 (mmm) REVERT: A 180 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 545 GLU cc_start: 0.7546 (pm20) cc_final: 0.7323 (pm20) REVERT: B 153 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8874 (mp) REVERT: B 403 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9003 (pp) REVERT: B 452 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8237 (pp) REVERT: C 739 GLU cc_start: 0.8774 (tp30) cc_final: 0.8249 (tp30) REVERT: D 480 ASN cc_start: 0.8397 (t0) cc_final: 0.7943 (t0) REVERT: D 513 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6781 (p0) REVERT: D 696 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.6038 (m-10) REVERT: D 794 LEU cc_start: 0.8420 (tp) cc_final: 0.8093 (pp) outliers start: 107 outliers final: 67 residues processed: 305 average time/residue: 0.1036 time to fit residues: 53.3957 Evaluate side-chains 282 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 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 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 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 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 507 ILE 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 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 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 513 ASN 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 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: 20.0000 chunk 224 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 HIS B 172 HIS ** 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 = 0.3585 r_free = 0.3585 target = 0.117110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092791 restraints weight = 41277.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092758 restraints weight = 27411.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093160 restraints weight = 27137.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093647 restraints weight = 21166.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094144 restraints weight = 19111.568| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 17060 Z= 0.322 Angle : 0.831 11.657 23415 Z= 0.425 Chirality : 0.050 0.317 2875 Planarity : 0.005 0.090 2951 Dihedral : 6.569 51.581 2441 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.78 % Favored : 88.17 % Rotamer: Outliers : 8.79 % Allowed : 21.45 % Favored : 69.77 % 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: -2.74 (0.16), residues: 2300 helix: -0.40 (0.17), residues: 854 sheet: -1.87 (0.33), residues: 232 loop : -2.99 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 389 TYR 0.022 0.002 TYR B 449 PHE 0.024 0.002 PHE D 635 TRP 0.027 0.002 TRP D 632 HIS 0.015 0.002 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.32 (17028) covalent geometry : angle 0.81729 / 0.42 (23341) SS BOND : bond 0.00865 / 0.54 ( 13) SS BOND : angle 2.32169 / 1.65 ( 26) hydrogen bonds : bond 0.06358 / 4.36 ( 637) hydrogen bonds : angle 5.72501 / 4.06 ( 1842) Misc. bond : bond 0.00384 / 0.19 ( 3) link_BETA1-4 : bond 0.00957 / 0.53 ( 6) link_BETA1-4 : angle 2.08605 / 1.24 ( 18) link_NAG-ASN : bond 0.00467 / 0.31 ( 10) link_NAG-ASN : angle 3.47706 / 2.54 ( 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 351 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 215 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8448 (pp) REVERT: A 180 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 455 CYS cc_start: 0.5205 (m) cc_final: 0.4956 (m) REVERT: B 153 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8891 (mp) REVERT: B 375 TRP cc_start: 0.9111 (OUTLIER) cc_final: 0.8670 (t-100) REVERT: B 403 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9045 (pp) REVERT: B 452 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8269 (pp) REVERT: D 696 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.6182 (m-10) REVERT: D 794 LEU cc_start: 0.8508 (tp) cc_final: 0.8134 (pp) outliers start: 136 outliers final: 102 residues processed: 321 average time/residue: 0.0961 time to fit residues: 53.1223 Evaluate side-chains 309 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 200 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP 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 194 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 648 THR 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 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 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 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 338 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 375 TRP 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 408 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 718 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 ILE 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 479 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 721 VAL Chi-restraints excluded: chain C residue 735 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 527 VAL Chi-restraints excluded: chain D residue 570 THR 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 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 734 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 36 optimal weight: 0.0050 chunk 214 optimal weight: 7.9990 chunk 24 optimal weight: 0.0370 chunk 113 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 overall best weight: 1.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 483 HIS B 672 GLN D 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.097286 restraints weight = 40324.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096635 restraints weight = 29377.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097209 restraints weight = 26132.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097640 restraints weight = 20593.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097849 restraints weight = 18890.794| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17060 Z= 0.133 Angle : 0.688 13.933 23415 Z= 0.345 Chirality : 0.045 0.280 2875 Planarity : 0.004 0.074 2951 Dihedral : 5.793 51.210 2436 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 5.75 % Allowed : 24.55 % Favored : 69.70 % 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: -2.28 (0.17), residues: 2300 helix: 0.00 (0.17), residues: 865 sheet: -1.75 (0.32), residues: 251 loop : -2.74 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.022 0.001 TYR D 759 PHE 0.018 0.001 PHE D 635 TRP 0.015 0.001 TRP C 792 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (17028) covalent geometry : angle 0.67548 / 0.34 (23341) SS BOND : bond 0.01490 / 1.18 ( 13) SS BOND : angle 1.60974 / 1.11 ( 26) hydrogen bonds : bond 0.04512 / 3.07 ( 637) hydrogen bonds : angle 4.90622 / 3.51 ( 1842) Misc. bond : bond 0.00390 / 0.19 ( 3) link_BETA1-4 : bond 0.01016 / 0.57 ( 6) link_BETA1-4 : angle 2.13853 / 1.27 ( 18) link_NAG-ASN : bond 0.00529 / 0.34 ( 10) link_NAG-ASN : angle 3.07441 / 2.26 ( 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 318 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 229 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5260 (m) cc_final: 0.5009 (m) REVERT: A 545 GLU cc_start: 0.7611 (pm20) cc_final: 0.7365 (pm20) REVERT: A 639 PHE cc_start: 0.8438 (t80) cc_final: 0.8054 (t80) REVERT: A 642 ILE cc_start: 0.9560 (tp) cc_final: 0.9207 (tp) REVERT: B 153 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 403 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9023 (pp) REVERT: B 452 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7963 (pp) REVERT: C 739 GLU cc_start: 0.8732 (tp30) cc_final: 0.8335 (tp30) REVERT: D 480 ASN cc_start: 0.8411 (t0) cc_final: 0.8012 (t0) REVERT: D 794 LEU cc_start: 0.8463 (tp) cc_final: 0.8157 (pp) outliers start: 89 outliers final: 55 residues processed: 294 average time/residue: 0.0963 time to fit residues: 48.5689 Evaluate side-chains 262 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 291 ASP 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 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 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 490 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 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 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 657 ILE Chi-restraints excluded: chain D residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 130 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 148 optimal weight: 30.0000 chunk 188 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN C 453 GLN D 612 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094820 restraints weight = 40556.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094392 restraints weight = 28921.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094839 restraints weight = 25849.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095342 restraints weight = 20433.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095508 restraints weight = 18475.454| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17060 Z= 0.216 Angle : 0.729 12.000 23415 Z= 0.367 Chirality : 0.046 0.269 2875 Planarity : 0.005 0.070 2951 Dihedral : 5.911 50.517 2436 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.13 % Favored : 88.83 % Rotamer: Outliers : 7.17 % Allowed : 23.45 % Favored : 69.38 % 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: -2.32 (0.17), residues: 2300 helix: 0.09 (0.17), residues: 864 sheet: -1.85 (0.32), residues: 252 loop : -2.84 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 673 TYR 0.024 0.002 TYR B 476 PHE 0.020 0.002 PHE D 635 TRP 0.018 0.001 TRP C 792 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (17028) covalent geometry : angle 0.71654 / 0.36 (23341) SS BOND : bond 0.01058 / 0.60 ( 13) SS BOND : angle 1.99609 / 1.41 ( 26) hydrogen bonds : bond 0.04789 / 3.28 ( 637) hydrogen bonds : angle 5.00922 / 3.56 ( 1842) Misc. bond : bond 0.00366 / 0.18 ( 3) link_BETA1-4 : bond 0.00767 / 0.44 ( 6) link_BETA1-4 : angle 2.00105 / 1.17 ( 18) link_NAG-ASN : bond 0.00365 / 0.25 ( 10) link_NAG-ASN : angle 3.14332 / 2.27 ( 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 324 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 213 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 455 CYS cc_start: 0.5337 (m) cc_final: 0.5118 (m) REVERT: A 639 PHE cc_start: 0.8436 (t80) cc_final: 0.8065 (t80) REVERT: A 642 ILE cc_start: 0.9561 (tp) cc_final: 0.9185 (tp) REVERT: B 153 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8884 (mp) REVERT: B 403 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9062 (pp) REVERT: B 452 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8171 (pp) REVERT: C 739 GLU cc_start: 0.8774 (tp30) cc_final: 0.8412 (tp30) REVERT: D 480 ASN cc_start: 0.8474 (t0) cc_final: 0.8058 (t0) REVERT: D 794 LEU cc_start: 0.8435 (tp) cc_final: 0.8173 (pp) outliers start: 111 outliers final: 82 residues processed: 295 average time/residue: 0.0965 time to fit residues: 49.0854 Evaluate side-chains 289 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 203 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 181 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 239 ASN 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 748 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 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 291 ASP 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 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 631 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 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 744 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 612 ASN 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 733 LEU Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 814 ASN 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=3.00 ------------------------------------------------------------------------------- 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: 10.0000 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN C 705 HIS D 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095965 restraints weight = 40251.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095429 restraints weight = 28686.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095973 restraints weight = 25697.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096364 restraints weight = 20514.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096563 restraints weight = 18801.882| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2134 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= 0.162 Angle : 0.713 12.461 23415 Z= 0.356 Chirality : 0.046 0.270 2875 Planarity : 0.004 0.068 2951 Dihedral : 5.814 50.585 2436 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 7.17 % Allowed : 24.61 % Favored : 68.22 % 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: -2.16 (0.17), residues: 2300 helix: 0.28 (0.18), residues: 851 sheet: -1.73 (0.33), residues: 240 loop : -2.78 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 671 TYR 0.020 0.001 TYR B 476 PHE 0.021 0.001 PHE D 635 TRP 0.024 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17028) covalent geometry : angle 0.69727 / 0.35 (23341) SS BOND : bond 0.00526 / 0.39 ( 13) SS BOND : angle 2.78738 / 2.04 ( 26) hydrogen bonds : bond 0.04397 / 3.00 ( 637) hydrogen bonds : angle 4.85779 / 3.49 ( 1842) Misc. bond : bond 0.00366 / 0.18 ( 3) link_BETA1-4 : bond 0.00978 / 0.53 ( 6) link_BETA1-4 : angle 2.01820 / 1.19 ( 18) link_NAG-ASN : bond 0.00392 / 0.26 ( 10) link_NAG-ASN : angle 3.10962 / 2.28 ( 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 326 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 215 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8560 (tt) REVERT: A 455 CYS cc_start: 0.5315 (m) cc_final: 0.5079 (m) REVERT: A 639 PHE cc_start: 0.8450 (t80) cc_final: 0.8060 (t80) REVERT: A 642 ILE cc_start: 0.9539 (tp) cc_final: 0.9156 (tp) REVERT: B 153 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8879 (mp) REVERT: B 403 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9051 (pp) REVERT: B 452 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8059 (pp) REVERT: C 739 GLU cc_start: 0.8740 (tp30) cc_final: 0.8406 (tp30) REVERT: D 480 ASN cc_start: 0.8437 (t0) cc_final: 0.8049 (t0) REVERT: D 794 LEU cc_start: 0.8478 (tp) cc_final: 0.8152 (pp) outliers start: 111 outliers final: 88 residues processed: 298 average time/residue: 0.0992 time to fit residues: 50.6922 Evaluate side-chains 300 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 208 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 293 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 521 ASN 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 752 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 153 LEU 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 359 VAL 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 511 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 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 453 GLN Chi-restraints excluded: chain C residue 472 PHE 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 679 PHE Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 657 ILE 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 822 LEU 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: 8.9990 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 206 optimal weight: 0.0770 chunk 120 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN C 650 ASN C 705 HIS D 612 ASN D 646 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097955 restraints weight = 40358.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098048 restraints weight = 28633.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098783 restraints weight = 22704.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099053 restraints weight = 19266.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099209 restraints weight = 17873.987| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2265 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= 0.119 Angle : 0.678 12.424 23415 Z= 0.335 Chirality : 0.045 0.335 2875 Planarity : 0.004 0.065 2951 Dihedral : 5.560 49.937 2436 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 5.88 % Allowed : 26.29 % Favored : 67.83 % 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: -1.96 (0.17), residues: 2300 helix: 0.41 (0.18), residues: 874 sheet: -1.56 (0.32), residues: 245 loop : -2.70 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 763 TYR 0.016 0.001 TYR B 476 PHE 0.024 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/Z covalent geometry : bond 0.00265 / 0.12 (17028) covalent geometry : angle 0.66467 / 0.33 (23341) SS BOND : bond 0.00403 / 0.30 ( 13) SS BOND : angle 1.82464 / 1.29 ( 26) hydrogen bonds : bond 0.03810 / 2.59 ( 637) hydrogen bonds : angle 4.58021 / 3.31 ( 1842) Misc. bond : bond 0.00359 / 0.18 ( 3) link_BETA1-4 : bond 0.00918 / 0.53 ( 6) link_BETA1-4 : angle 2.01416 / 1.18 ( 18) link_NAG-ASN : bond 0.00647 / 0.40 ( 10) link_NAG-ASN : angle 3.10289 / 2.35 ( 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 316 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 225 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5272 (m) cc_final: 0.5034 (m) REVERT: A 639 PHE cc_start: 0.8404 (t80) cc_final: 0.8032 (t80) REVERT: A 642 ILE cc_start: 0.9483 (tp) cc_final: 0.9122 (tp) REVERT: B 153 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9125 (mp) REVERT: B 403 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9035 (pp) REVERT: B 452 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8002 (pp) REVERT: B 658 ASP cc_start: 0.7544 (m-30) cc_final: 0.6502 (p0) REVERT: C 739 GLU cc_start: 0.8689 (tp30) cc_final: 0.8357 (tp30) REVERT: D 480 ASN cc_start: 0.8308 (t0) cc_final: 0.7870 (t0) REVERT: D 794 LEU cc_start: 0.8330 (tp) cc_final: 0.8090 (pp) outliers start: 91 outliers final: 61 residues processed: 293 average time/residue: 0.0990 time to fit residues: 49.4647 Evaluate side-chains 275 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 211 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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 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 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 403 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL 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 C residue 472 PHE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 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 609 LEU 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: 4.9990 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 153 optimal weight: 0.1980 chunk 213 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097749 restraints weight = 40239.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097045 restraints weight = 29159.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097633 restraints weight = 25838.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098072 restraints weight = 20402.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098279 restraints weight = 18762.360| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2382 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= 0.133 Angle : 0.677 12.774 23415 Z= 0.333 Chirality : 0.045 0.284 2875 Planarity : 0.004 0.067 2951 Dihedral : 5.464 49.368 2436 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 5.81 % Allowed : 26.29 % Favored : 67.89 % 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: -1.85 (0.17), residues: 2300 helix: 0.53 (0.18), residues: 872 sheet: -1.51 (0.32), residues: 245 loop : -2.65 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 523 TYR 0.030 0.001 TYR A 647 PHE 0.027 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/Z covalent geometry : bond 0.00310 / 0.13 (17028) covalent geometry : angle 0.66405 / 0.33 (23341) SS BOND : bond 0.00414 / 0.30 ( 13) SS BOND : angle 1.75169 / 1.24 ( 26) hydrogen bonds : bond 0.03771 / 2.57 ( 637) hydrogen bonds : angle 4.51503 / 3.25 ( 1842) Misc. bond : bond 0.00350 / 0.17 ( 3) link_BETA1-4 : bond 0.00927 / 0.52 ( 6) link_BETA1-4 : angle 1.96861 / 1.15 ( 18) link_NAG-ASN : bond 0.00508 / 0.33 ( 10) link_NAG-ASN : angle 3.03345 / 2.29 ( 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 310 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 220 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 CYS cc_start: 0.5316 (m) cc_final: 0.5067 (m) REVERT: A 639 PHE cc_start: 0.8428 (t80) cc_final: 0.8041 (t80) REVERT: A 642 ILE cc_start: 0.9438 (tp) cc_final: 0.9159 (tp) REVERT: B 153 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8908 (mp) REVERT: B 403 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9039 (pp) REVERT: B 452 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8022 (pp) REVERT: B 628 MET cc_start: 0.7428 (ttt) cc_final: 0.6967 (ttm) REVERT: B 658 ASP cc_start: 0.7642 (m-30) cc_final: 0.6528 (p0) REVERT: C 739 GLU cc_start: 0.8714 (tp30) cc_final: 0.8390 (tp30) REVERT: D 480 ASN cc_start: 0.8386 (t0) cc_final: 0.7998 (t0) REVERT: D 556 TRP cc_start: 0.8389 (m100) cc_final: 0.8082 (m100) REVERT: D 794 LEU cc_start: 0.8383 (tp) cc_final: 0.8095 (pp) outliers start: 90 outliers final: 77 residues processed: 288 average time/residue: 0.0937 time to fit residues: 46.3499 Evaluate side-chains 287 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 207 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 141 VAL 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 218 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 296 LEU 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 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 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 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 359 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 511 THR 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 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 472 PHE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 792 TRP Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 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 798 CYS Chi-restraints excluded: chain D residue 830 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 85 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN C 650 ASN D 612 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095111 restraints weight = 40907.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095834 restraints weight = 28520.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095962 restraints weight = 24815.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097106 restraints weight = 20545.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097039 restraints weight = 17453.117| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17060 Z= 0.207 Angle : 0.732 13.319 23415 Z= 0.364 Chirality : 0.046 0.288 2875 Planarity : 0.005 0.074 2951 Dihedral : 5.680 50.143 2436 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 6.33 % Allowed : 26.29 % Favored : 67.38 % 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: -1.95 (0.17), residues: 2300 helix: 0.45 (0.18), residues: 872 sheet: -1.63 (0.32), residues: 260 loop : -2.70 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 671 TYR 0.031 0.002 TYR B 476 PHE 0.031 0.002 PHE D 635 TRP 0.020 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (17028) covalent geometry : angle 0.71943 / 0.36 (23341) SS BOND : bond 0.00468 / 0.34 ( 13) SS BOND : angle 2.00697 / 1.45 ( 26) hydrogen bonds : bond 0.04257 / 2.92 ( 637) hydrogen bonds : angle 4.69581 / 3.36 ( 1842) Misc. bond : bond 0.00358 / 0.18 ( 3) link_BETA1-4 : bond 0.00859 / 0.49 ( 6) link_BETA1-4 : angle 1.90846 / 1.10 ( 18) link_NAG-ASN : bond 0.00424 / 0.28 ( 10) link_NAG-ASN : angle 3.19092 / 2.39 ( 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 305 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 207 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 455 CYS cc_start: 0.5403 (m) cc_final: 0.5156 (m) REVERT: A 639 PHE cc_start: 0.8476 (t80) cc_final: 0.8107 (t80) REVERT: A 642 ILE cc_start: 0.9442 (tp) cc_final: 0.9159 (tp) REVERT: B 153 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8848 (mp) REVERT: B 403 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9065 (pp) REVERT: B 452 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8229 (pp) REVERT: B 628 MET cc_start: 0.7486 (ttt) cc_final: 0.6999 (ttm) REVERT: B 658 ASP cc_start: 0.7679 (m-30) cc_final: 0.6549 (p0) REVERT: D 480 ASN cc_start: 0.8415 (t0) cc_final: 0.8010 (t0) REVERT: D 556 TRP cc_start: 0.8420 (m100) cc_final: 0.8136 (m100) REVERT: D 696 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.5933 (m-10) REVERT: D 794 LEU cc_start: 0.8364 (tp) cc_final: 0.8091 (pp) outliers start: 98 outliers final: 85 residues processed: 283 average time/residue: 0.0978 time to fit residues: 47.3839 Evaluate side-chains 296 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 206 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 296 LEU 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 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 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 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 461 ILE Chi-restraints excluded: chain B residue 511 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 718 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 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 511 THR Chi-restraints excluded: chain D residue 524 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 756 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 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: 3.9990 chunk 97 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3642 r_free = 0.3642 target = 0.120930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095991 restraints weight = 40796.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096539 restraints weight = 27392.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096856 restraints weight = 25436.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097314 restraints weight = 20205.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097589 restraints weight = 18356.383| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17060 Z= 0.172 Angle : 0.717 13.422 23415 Z= 0.354 Chirality : 0.046 0.285 2875 Planarity : 0.005 0.070 2951 Dihedral : 5.654 50.606 2436 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 6.20 % Allowed : 26.55 % Favored : 67.25 % 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: -1.92 (0.17), residues: 2300 helix: 0.48 (0.17), residues: 870 sheet: -1.61 (0.31), residues: 260 loop : -2.67 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 389 TYR 0.028 0.001 TYR B 476 PHE 0.031 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/Z covalent geometry : bond 0.00406 / 0.17 (17028) covalent geometry : angle 0.70438 / 0.35 (23341) SS BOND : bond 0.00463 / 0.34 ( 13) SS BOND : angle 1.84329 / 1.32 ( 26) hydrogen bonds : bond 0.04076 / 2.79 ( 637) hydrogen bonds : angle 4.61867 / 3.30 ( 1842) Misc. bond : bond 0.00359 / 0.18 ( 3) link_BETA1-4 : bond 0.00908 / 0.52 ( 6) link_BETA1-4 : angle 1.90759 / 1.10 ( 18) link_NAG-ASN : bond 0.00422 / 0.27 ( 10) link_NAG-ASN : angle 3.15491 / 2.37 ( 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 303 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 207 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 455 CYS cc_start: 0.5476 (m) cc_final: 0.5218 (m) REVERT: A 639 PHE cc_start: 0.8486 (t80) cc_final: 0.8106 (t80) REVERT: A 641 MET cc_start: 0.8860 (tpp) cc_final: 0.8635 (tpp) REVERT: A 642 ILE cc_start: 0.9413 (tp) cc_final: 0.9141 (tp) REVERT: B 153 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8835 (mp) REVERT: B 403 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9063 (pp) REVERT: B 452 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8171 (pp) REVERT: B 628 MET cc_start: 0.7458 (ttt) cc_final: 0.6980 (ttm) REVERT: B 658 ASP cc_start: 0.7675 (m-30) cc_final: 0.6543 (p0) REVERT: C 739 GLU cc_start: 0.8751 (tp30) cc_final: 0.8432 (tp30) REVERT: D 480 ASN cc_start: 0.8434 (t0) cc_final: 0.8031 (t0) REVERT: D 556 TRP cc_start: 0.8393 (m100) cc_final: 0.8130 (m100) REVERT: D 699 MET cc_start: 0.8072 (tpt) cc_final: 0.7501 (mpp) REVERT: D 794 LEU cc_start: 0.8379 (tp) cc_final: 0.8084 (pp) outliers start: 96 outliers final: 88 residues processed: 283 average time/residue: 0.1013 time to fit residues: 48.7236 Evaluate side-chains 298 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 206 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 218 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 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 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 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 415 ILE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 750 SER 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 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 511 THR Chi-restraints excluded: chain D residue 524 VAL 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 798 CYS Chi-restraints excluded: chain D residue 814 ASN 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: 2.9990 chunk 124 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 94 optimal weight: 0.0040 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 0.0270 chunk 213 optimal weight: 10.0000 chunk 134 optimal weight: 0.0570 chunk 18 optimal weight: 8.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3643 r_free = 0.3643 target = 0.121005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096010 restraints weight = 40499.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096511 restraints weight = 27556.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096656 restraints weight = 25163.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098158 restraints weight = 20684.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098043 restraints weight = 16497.020| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 17060 Z= 0.186 Angle : 0.885 59.191 23415 Z= 0.482 Chirality : 0.045 0.342 2875 Planarity : 0.005 0.062 2951 Dihedral : 5.683 50.626 2436 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.35 % Favored : 89.61 % Rotamer: Outliers : 6.14 % Allowed : 26.74 % Favored : 67.12 % Cbeta Deviations : 0.05 % 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: -1.90 (0.17), residues: 2300 helix: 0.49 (0.17), residues: 870 sheet: -1.61 (0.31), residues: 260 loop : -2.67 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 679 TYR 0.025 0.001 TYR B 476 PHE 0.027 0.001 PHE D 635 TRP 0.017 0.001 TRP D 632 HIS 0.014 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (17028) covalent geometry : angle 0.87529 / 0.48 (23341) SS BOND : bond 0.00413 / 0.30 ( 13) SS BOND : angle 1.80125 / 1.28 ( 26) hydrogen bonds : bond 0.04022 / 2.75 ( 637) hydrogen bonds : angle 4.61402 / 3.30 ( 1842) Misc. bond : bond 0.00373 / 0.18 ( 3) link_BETA1-4 : bond 0.00896 / 0.53 ( 6) link_BETA1-4 : angle 1.89120 / 1.08 ( 18) link_NAG-ASN : bond 0.00414 / 0.27 ( 10) link_NAG-ASN : angle 3.15176 / 2.37 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.26 seconds wall clock time: 51 minutes 59.54 seconds (3119.54 seconds total)