Starting phenix.real_space_refine on Sun Jun 15 22:28:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szi_40917/06_2025/8szi_40917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szi_40917/06_2025/8szi_40917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8szi_40917/06_2025/8szi_40917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szi_40917/06_2025/8szi_40917.map" model { file = "/net/cci-nas-00/data/ceres_data/8szi_40917/06_2025/8szi_40917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szi_40917/06_2025/8szi_40917.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.060 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 C 11526 2.51 5 N 2932 2.21 5 O 3294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17868 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1765 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2509 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 6538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 826, 6524 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 32, 'TRANS': 793} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 826, 6524 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 32, 'TRANS': 793} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 6676 Chain: "B" Number of atoms: 6327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6327 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 31, 'TRANS': 770} Chain breaks: 3 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1005 "'] Classifications: {'peptide': 2, 'undetermined': 5} Modifications used: {'COO': 2} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 132 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 2, 'PCW': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1407 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 818 " occ=0.70 ... (26 atoms not shown) pdb=" CH2BTRP A 818 " occ=0.30 Time building chain proxies: 17.79, per 1000 atoms: 1.00 Number of scatterers: 17868 At special positions: 0 Unit cell: (99.7855, 118.007, 249.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 108 16.00 P 4 15.00 O 3294 8.00 N 2932 7.00 C 11526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.06 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=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1002 " - " ASN A 468 " " NAG B1403 " - " ASN B 468 " " NAG B1404 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 3.1 seconds 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 23 sheets defined 43.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 207 through 213 removed outlier: 4.171A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.941A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.945A pdb=" N PHE C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.671A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 329 through 351 Processing helix chain 'D' and resid 4 through 25 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 24 removed outlier: 3.686A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.624A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'A' and resid 64 through 83 removed outlier: 3.680A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.503A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.788A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.587A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.522A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.128A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 272 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.509A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.544A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.678A pdb=" N ILE A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.633A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.646A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 673 through 678 removed outlier: 3.940A pdb=" N ARG A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 708 removed outlier: 4.040A pdb=" N ALA A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 746 removed outlier: 3.665A pdb=" N GLN A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.558A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 821 Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 831 through 862 removed outlier: 3.624A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 867 removed outlier: 3.601A pdb=" N ARG A 866 " --> pdb=" O LYS A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 878 Processing helix chain 'B' and resid 66 through 84 removed outlier: 3.729A pdb=" N TRP B 70 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.603A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.838A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.078A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.629A pdb=" N VAL B 258 " --> pdb=" O HIS B 254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 416 through 436 removed outlier: 3.571A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.913A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.768A pdb=" N GLY B 532 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.681A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.921A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 673 through 698 removed outlier: 4.749A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix Processing helix chain 'B' and resid 702 through 707 removed outlier: 4.399A pdb=" N PHE B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.607A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 732 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 794 removed outlier: 3.841A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 828 removed outlier: 3.721A pdb=" N ASN B 802 " --> pdb=" O PRO B 798 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 803 " --> pdb=" O GLU B 799 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 805 " --> pdb=" O PHE B 801 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 830 through 833 Processing helix chain 'B' and resid 834 through 861 removed outlier: 3.745A pdb=" N VAL B 838 " --> pdb=" O SER B 834 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 876 Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.698A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 51 removed outlier: 7.143A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 6.893A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.884A pdb=" N ALA D 104 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 112 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.920A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.777A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.960A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 252 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.845A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.737A pdb=" N TYR A 95 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.090A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.891A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB4, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB5, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AB6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.214A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.728A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 37 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.068A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP B 293 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N PHE B 320 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA B 295 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AC3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AC4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AC5, first strand: chain 'B' and resid 602 through 604 removed outlier: 3.736A pdb=" N ILE B 763 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 762 " --> pdb=" O ASN B 753 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 751 " --> pdb=" O THR B 764 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2197 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: 6.33 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2887 1.32 - 1.44: 5110 1.44 - 1.57: 10126 1.57 - 1.70: 22 1.70 - 1.83: 136 Bond restraints: 18281 Sorted by residual: bond pdb=" C31 PCW B1402 " pdb=" O2 PCW B1402 " ideal model delta sigma weight residual 1.333 1.488 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" C31 PCW A1001 " pdb=" O2 PCW A1001 " ideal model delta sigma weight residual 1.333 1.485 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C ASN B 802 " pdb=" O ASN B 802 " ideal model delta sigma weight residual 1.233 1.315 -0.082 1.29e-02 6.01e+03 4.09e+01 bond pdb=" C31 PCW B1402 " pdb=" C32 PCW B1402 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C31 PCW A1001 " pdb=" C32 PCW A1001 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 18276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 24722 5.01 - 10.02: 61 10.02 - 15.03: 5 15.03 - 20.05: 2 20.05 - 25.06: 2 Bond angle restraints: 24792 Sorted by residual: angle pdb=" C18 PCW B1402 " pdb=" C19 PCW B1402 " pdb=" C20 PCW B1402 " ideal model delta sigma weight residual 127.82 152.88 -25.06 3.00e+00 1.11e-01 6.98e+01 angle pdb=" C18 PCW A1001 " pdb=" C19 PCW A1001 " pdb=" C20 PCW A1001 " ideal model delta sigma weight residual 127.82 152.77 -24.95 3.00e+00 1.11e-01 6.92e+01 angle pdb=" N ASN A 118 " pdb=" CA ASN A 118 " pdb=" C ASN A 118 " ideal model delta sigma weight residual 112.38 104.38 8.00 1.22e+00 6.72e-01 4.30e+01 angle pdb=" C GLU A 232 " pdb=" N ARG A 233 " pdb=" CA ARG A 233 " ideal model delta sigma weight residual 122.65 113.56 9.09 1.60e+00 3.91e-01 3.23e+01 angle pdb=" N PHE A 714 " pdb=" CA PHE A 714 " pdb=" C PHE A 714 " ideal model delta sigma weight residual 113.38 106.41 6.97 1.23e+00 6.61e-01 3.21e+01 ... (remaining 24787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 10219 20.83 - 41.67: 645 41.67 - 62.50: 85 62.50 - 83.34: 19 83.34 - 104.17: 7 Dihedral angle restraints: 10975 sinusoidal: 4430 harmonic: 6545 Sorted by residual: dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 177.76 -84.76 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -167.54 81.54 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -39.73 -46.27 1 1.00e+01 1.00e-02 2.96e+01 ... (remaining 10972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.037: 2803 1.037 - 2.074: 0 2.074 - 3.111: 0 3.111 - 4.148: 0 4.148 - 5.185: 1 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C2 PCW A1001 " pdb=" C1 PCW A1001 " pdb=" C3 PCW A1001 " pdb=" O2 PCW A1001 " both_signs ideal model delta sigma weight residual False -2.32 2.86 -5.19 2.00e-01 2.50e+01 6.72e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C2 PCW B1402 " pdb=" C1 PCW B1402 " pdb=" C3 PCW B1402 " pdb=" O2 PCW B1402 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 2801 not shown) Planarity restraints: 3127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.338 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG H 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.257 2.00e-02 2.50e+03 2.16e-01 5.81e+02 pdb=" C7 NAG H 1 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.362 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 817 " -0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C VAL A 817 " 0.092 2.00e-02 2.50e+03 pdb=" O VAL A 817 " -0.034 2.00e-02 2.50e+03 pdb=" N ATRP A 818 " -0.032 2.00e-02 2.50e+03 ... (remaining 3124 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 57 2.56 - 3.14: 13370 3.14 - 3.73: 25376 3.73 - 4.31: 36003 4.31 - 4.90: 61447 Nonbonded interactions: 136253 Sorted by model distance: nonbonded pdb=" O LEU A 88 " pdb="CA CA A1003 " model vdw 1.971 2.510 nonbonded pdb=" O LEU B 88 " pdb="CA CA B1405 " model vdw 2.085 2.510 nonbonded pdb=" OE2 GLU C 318 " pdb=" OH TYR C 320 " model vdw 2.196 3.040 nonbonded pdb=" NH1 ARG A 69 " pdb=" O PRO A 407 " model vdw 2.203 3.120 nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.210 3.040 ... (remaining 136248 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 'A' and (resid 20 through 362 or resid 392 through 516 or (resid 517 and \ (name N or name CA or name C or name O or name CB )) or resid 518 through 586 or \ (resid 587 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 8 through 601 or (resid 602 and (name N or name CA or name C or name O or name C \ B )) or resid 603 or (resid 604 and (name N or name CA or name C or name O or na \ me CB )) or resid 605 through 704 or (resid 705 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 708 or (resid 709 and (name N or n \ ame CA or name C or name O or name CB )) or resid 722 through 798 or (resid 799 \ and (name N or name CA or name C or name O or name CB )) or resid 800 through 81 \ 7 or resid 819 through 861 or (resid 862 through 863 and (name N or name CA or n \ ame C or name O or name CB )) or resid 864 through 865 or (resid 866 through 867 \ and (name N or name CA or name C or name O or name CB )) or resid 868 through 8 \ 70 or (resid 871 through 873 and (name N or name CA or name C or name O or name \ CB )) or resid 874 through 876 or resid 1002 through 1006)) selection = (chain 'B' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 47 or (resid 48 and (name N or name CA or name C or name \ O or name CB )) or resid 49 through 118 or (resid 119 through 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 361 or (resid 36 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 392 through \ 498 or (resid 499 through 500 and (name N or name CA or name C or name O or name \ CB )) or resid 501 through 591 or (resid 592 and (name N or name CA or name C o \ r name O or name CB )) or resid 593 through 817 or resid 819 through 876 or resi \ d 1404 through 1408)) } ncs_group { reference = chain 'F' selection = 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=0.30 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: 7.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 51.160 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 : 0.008 0.155 18308 Z= 0.500 Angle : 0.970 25.057 24855 Z= 0.655 Chirality : 0.117 5.185 2804 Planarity : 0.008 0.293 3121 Dihedral : 13.695 104.170 6683 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.05 % Allowed : 1.61 % Favored : 98.34 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2227 helix: 1.43 (0.18), residues: 871 sheet: -0.48 (0.26), residues: 383 loop : -0.63 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 719 HIS 0.007 0.001 HIS A 715 PHE 0.025 0.001 PHE A 814 TYR 0.038 0.001 TYR A 425 ARG 0.003 0.000 ARG B 551 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 6) link_NAG-ASN : angle 2.57753 ( 18) link_BETA1-4 : bond 0.00271 ( 3) link_BETA1-4 : angle 1.35610 ( 9) hydrogen bonds : bond 0.21817 ( 760) hydrogen bonds : angle 6.30726 ( 2197) SS BOND : bond 0.00824 ( 18) SS BOND : angle 1.76924 ( 36) covalent geometry : bond 0.00750 (18281) covalent geometry : angle 0.96560 (24792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: C 230 TYR cc_start: 0.7454 (p90) cc_final: 0.7163 (p90) REVERT: A 58 VAL cc_start: 0.8667 (p) cc_final: 0.8424 (m) REVERT: A 189 ASN cc_start: 0.7770 (p0) cc_final: 0.7568 (p0) REVERT: A 410 ASP cc_start: 0.8131 (m-30) cc_final: 0.7834 (m-30) REVERT: A 663 SER cc_start: 0.8756 (t) cc_final: 0.8188 (p) REVERT: A 704 LEU cc_start: 0.8634 (tp) cc_final: 0.8293 (mt) REVERT: B 54 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7326 (ttm110) REVERT: B 58 VAL cc_start: 0.8156 (p) cc_final: 0.7943 (m) REVERT: B 251 GLU cc_start: 0.7293 (pt0) cc_final: 0.7063 (pt0) REVERT: B 341 LYS cc_start: 0.7588 (mtmt) cc_final: 0.7384 (mmtt) REVERT: B 357 ASN cc_start: 0.8375 (t0) cc_final: 0.8097 (t0) REVERT: B 643 VAL cc_start: 0.7562 (m) cc_final: 0.7337 (t) REVERT: B 706 PHE cc_start: 0.6185 (t80) cc_final: 0.5715 (t80) REVERT: B 771 MET cc_start: 0.5157 (mmm) cc_final: 0.4944 (mtt) outliers start: 1 outliers final: 1 residues processed: 334 average time/residue: 0.3206 time to fit residues: 158.0339 Evaluate side-chains 214 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 174 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 75 GLN D 175 GLN A 193 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 117 GLN B 463 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.076081 restraints weight = 63477.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.077645 restraints weight = 98906.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077959 restraints weight = 69054.687| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18308 Z= 0.119 Angle : 0.532 8.545 24855 Z= 0.283 Chirality : 0.042 0.165 2804 Planarity : 0.004 0.045 3121 Dihedral : 8.147 82.810 2751 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.91 % Allowed : 6.53 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2227 helix: 1.91 (0.17), residues: 878 sheet: -0.45 (0.26), residues: 382 loop : -0.69 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 719 HIS 0.014 0.001 HIS A 766 PHE 0.027 0.001 PHE A 789 TYR 0.012 0.001 TYR B 421 ARG 0.007 0.001 ARG D 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 1.60951 ( 18) link_BETA1-4 : bond 0.00204 ( 3) link_BETA1-4 : angle 2.04317 ( 9) hydrogen bonds : bond 0.05829 ( 760) hydrogen bonds : angle 4.34095 ( 2197) SS BOND : bond 0.00358 ( 18) SS BOND : angle 1.55328 ( 36) covalent geometry : bond 0.00236 (18281) covalent geometry : angle 0.52619 (24792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7785 (mtm180) REVERT: D 14 LEU cc_start: 0.7249 (mm) cc_final: 0.6847 (mp) REVERT: D 297 TRP cc_start: 0.8279 (m100) cc_final: 0.8053 (m100) REVERT: A 663 SER cc_start: 0.8694 (t) cc_final: 0.8216 (p) REVERT: A 704 LEU cc_start: 0.8356 (tp) cc_final: 0.8031 (mt) REVERT: B 58 VAL cc_start: 0.8284 (p) cc_final: 0.7973 (m) REVERT: B 357 ASN cc_start: 0.8338 (t0) cc_final: 0.7948 (t0) REVERT: B 706 PHE cc_start: 0.6081 (t80) cc_final: 0.5734 (t80) outliers start: 17 outliers final: 9 residues processed: 229 average time/residue: 0.3331 time to fit residues: 113.5756 Evaluate side-chains 197 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 135 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 432 GLN B 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072276 restraints weight = 67393.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074432 restraints weight = 79457.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074806 restraints weight = 60372.111| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18308 Z= 0.136 Angle : 0.513 6.906 24855 Z= 0.273 Chirality : 0.042 0.188 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.602 77.937 2751 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.23 % Allowed : 8.08 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2227 helix: 2.00 (0.17), residues: 879 sheet: -0.50 (0.26), residues: 384 loop : -0.72 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 PHE 0.018 0.001 PHE A 814 TYR 0.014 0.001 TYR B 421 ARG 0.005 0.000 ARG A 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 6) link_NAG-ASN : angle 1.67164 ( 18) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 1.44220 ( 9) hydrogen bonds : bond 0.05615 ( 760) hydrogen bonds : angle 4.17268 ( 2197) SS BOND : bond 0.00282 ( 18) SS BOND : angle 1.51648 ( 36) covalent geometry : bond 0.00309 (18281) covalent geometry : angle 0.50738 (24792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.756 Fit side-chains REVERT: C 24 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7983 (mtm180) REVERT: A 253 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7216 (mm-40) REVERT: A 663 SER cc_start: 0.8713 (t) cc_final: 0.8192 (p) REVERT: A 704 LEU cc_start: 0.8507 (tp) cc_final: 0.8177 (mt) REVERT: B 58 VAL cc_start: 0.8332 (p) cc_final: 0.8058 (m) REVERT: B 643 VAL cc_start: 0.7476 (m) cc_final: 0.7225 (t) outliers start: 23 outliers final: 13 residues processed: 216 average time/residue: 0.3177 time to fit residues: 102.9650 Evaluate side-chains 199 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 75 GLN D 175 GLN A 117 GLN A 193 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 357 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.072462 restraints weight = 65974.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074906 restraints weight = 77813.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075165 restraints weight = 54579.679| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18308 Z= 0.119 Angle : 0.490 8.280 24855 Z= 0.261 Chirality : 0.042 0.178 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.168 71.550 2751 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.39 % Allowed : 9.31 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2227 helix: 2.06 (0.17), residues: 881 sheet: -0.52 (0.26), residues: 388 loop : -0.78 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 PHE 0.027 0.001 PHE A 789 TYR 0.014 0.001 TYR B 421 ARG 0.005 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 6) link_NAG-ASN : angle 1.65522 ( 18) link_BETA1-4 : bond 0.00205 ( 3) link_BETA1-4 : angle 1.39073 ( 9) hydrogen bonds : bond 0.04984 ( 760) hydrogen bonds : angle 3.96973 ( 2197) SS BOND : bond 0.00322 ( 18) SS BOND : angle 1.45883 ( 36) covalent geometry : bond 0.00266 (18281) covalent geometry : angle 0.48515 (24792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8212 (mtm180) cc_final: 0.7979 (mtm180) REVERT: D 14 LEU cc_start: 0.7571 (mm) cc_final: 0.7238 (mm) REVERT: D 181 THR cc_start: 0.8227 (p) cc_final: 0.7979 (t) REVERT: D 297 TRP cc_start: 0.8300 (m100) cc_final: 0.8059 (m100) REVERT: A 657 SER cc_start: 0.8698 (t) cc_final: 0.8464 (m) REVERT: A 663 SER cc_start: 0.8702 (t) cc_final: 0.8190 (p) REVERT: A 716 ARG cc_start: 0.7670 (tpp-160) cc_final: 0.7244 (mmt-90) REVERT: B 58 VAL cc_start: 0.8334 (p) cc_final: 0.8054 (m) REVERT: B 688 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7141 (m-80) outliers start: 26 outliers final: 15 residues processed: 212 average time/residue: 0.3207 time to fit residues: 101.4958 Evaluate side-chains 204 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 133 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN A 309 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073131 restraints weight = 64733.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074829 restraints weight = 94582.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.075102 restraints weight = 69733.912| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18308 Z= 0.138 Angle : 0.513 7.828 24855 Z= 0.274 Chirality : 0.042 0.278 2804 Planarity : 0.004 0.049 3121 Dihedral : 6.922 67.557 2751 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.44 % Allowed : 10.22 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2227 helix: 2.05 (0.17), residues: 881 sheet: -0.56 (0.26), residues: 388 loop : -0.83 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 PHE 0.021 0.001 PHE B 729 TYR 0.015 0.001 TYR B 421 ARG 0.006 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.71491 ( 18) link_BETA1-4 : bond 0.00146 ( 3) link_BETA1-4 : angle 1.49538 ( 9) hydrogen bonds : bond 0.05167 ( 760) hydrogen bonds : angle 3.95383 ( 2197) SS BOND : bond 0.00173 ( 18) SS BOND : angle 1.52174 ( 36) covalent geometry : bond 0.00321 (18281) covalent geometry : angle 0.50761 (24792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6939 (mm) REVERT: D 181 THR cc_start: 0.8153 (p) cc_final: 0.7936 (t) REVERT: A 570 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.6330 (t0) REVERT: A 657 SER cc_start: 0.8659 (t) cc_final: 0.8410 (m) REVERT: A 663 SER cc_start: 0.8693 (t) cc_final: 0.8209 (p) REVERT: B 58 VAL cc_start: 0.8356 (p) cc_final: 0.8075 (m) REVERT: B 270 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8231 (t80) REVERT: B 688 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7124 (m-80) outliers start: 27 outliers final: 20 residues processed: 212 average time/residue: 0.3166 time to fit residues: 100.7857 Evaluate side-chains 205 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 218 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 162 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.089585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073251 restraints weight = 65533.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075222 restraints weight = 90921.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075687 restraints weight = 67110.736| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18308 Z= 0.116 Angle : 0.494 8.258 24855 Z= 0.262 Chirality : 0.041 0.207 2804 Planarity : 0.003 0.048 3121 Dihedral : 6.749 65.986 2751 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.39 % Allowed : 10.65 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2227 helix: 2.11 (0.17), residues: 882 sheet: -0.54 (0.26), residues: 384 loop : -0.85 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 99 HIS 0.013 0.001 HIS B 463 PHE 0.028 0.001 PHE A 789 TYR 0.014 0.001 TYR B 421 ARG 0.004 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 6) link_NAG-ASN : angle 1.68012 ( 18) link_BETA1-4 : bond 0.00222 ( 3) link_BETA1-4 : angle 1.41426 ( 9) hydrogen bonds : bond 0.04786 ( 760) hydrogen bonds : angle 3.88378 ( 2197) SS BOND : bond 0.00153 ( 18) SS BOND : angle 1.43260 ( 36) covalent geometry : bond 0.00258 (18281) covalent geometry : angle 0.48858 (24792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: A 570 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.6274 (t0) REVERT: A 657 SER cc_start: 0.8663 (t) cc_final: 0.8405 (m) REVERT: A 663 SER cc_start: 0.8670 (t) cc_final: 0.8210 (p) REVERT: B 58 VAL cc_start: 0.8361 (p) cc_final: 0.8079 (m) REVERT: B 270 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8169 (t80) REVERT: B 688 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: B 818 TRP cc_start: 0.8413 (m100) cc_final: 0.8150 (m100) outliers start: 26 outliers final: 16 residues processed: 199 average time/residue: 0.3152 time to fit residues: 94.5483 Evaluate side-chains 199 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 74 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.088811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072610 restraints weight = 57283.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072328 restraints weight = 68563.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073026 restraints weight = 55891.828| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18308 Z= 0.144 Angle : 0.519 8.265 24855 Z= 0.275 Chirality : 0.043 0.205 2804 Planarity : 0.004 0.049 3121 Dihedral : 6.703 63.458 2751 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.34 % Allowed : 11.34 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2227 helix: 2.05 (0.17), residues: 882 sheet: -0.54 (0.26), residues: 386 loop : -0.89 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 719 HIS 0.013 0.001 HIS A 766 PHE 0.025 0.001 PHE A 733 TYR 0.015 0.001 TYR B 421 ARG 0.006 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 6) link_NAG-ASN : angle 1.74019 ( 18) link_BETA1-4 : bond 0.00198 ( 3) link_BETA1-4 : angle 1.51849 ( 9) hydrogen bonds : bond 0.05147 ( 760) hydrogen bonds : angle 3.94089 ( 2197) SS BOND : bond 0.00185 ( 18) SS BOND : angle 1.50419 ( 36) covalent geometry : bond 0.00340 (18281) covalent geometry : angle 0.51357 (24792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 2.081 Fit side-chains revert: symmetry clash REVERT: C 290 TYR cc_start: 0.6468 (p90) cc_final: 0.6237 (p90) REVERT: A 570 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6402 (t0) REVERT: A 657 SER cc_start: 0.8649 (t) cc_final: 0.8409 (m) REVERT: A 663 SER cc_start: 0.8704 (t) cc_final: 0.8201 (p) REVERT: B 58 VAL cc_start: 0.8380 (p) cc_final: 0.8102 (m) REVERT: B 270 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8259 (t80) REVERT: B 688 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: B 818 TRP cc_start: 0.8436 (m100) cc_final: 0.8170 (m100) outliers start: 25 outliers final: 18 residues processed: 207 average time/residue: 0.3323 time to fit residues: 103.1253 Evaluate side-chains 204 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 21 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 75 GLN A 117 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.089521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072310 restraints weight = 62908.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.072792 restraints weight = 68695.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073214 restraints weight = 63731.509| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18308 Z= 0.113 Angle : 0.497 9.395 24855 Z= 0.263 Chirality : 0.041 0.188 2804 Planarity : 0.003 0.047 3121 Dihedral : 6.538 63.205 2751 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.18 % Allowed : 12.41 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2227 helix: 2.18 (0.17), residues: 882 sheet: -0.49 (0.26), residues: 382 loop : -0.84 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 PHE 0.032 0.001 PHE A 733 TYR 0.014 0.001 TYR B 421 ARG 0.007 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 6) link_NAG-ASN : angle 1.67994 ( 18) link_BETA1-4 : bond 0.00173 ( 3) link_BETA1-4 : angle 1.39503 ( 9) hydrogen bonds : bond 0.04593 ( 760) hydrogen bonds : angle 3.81651 ( 2197) SS BOND : bond 0.00152 ( 18) SS BOND : angle 1.40246 ( 36) covalent geometry : bond 0.00252 (18281) covalent geometry : angle 0.49192 (24792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 2.010 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8376 (tptt) cc_final: 0.7678 (ttpp) REVERT: C 290 TYR cc_start: 0.6473 (p90) cc_final: 0.6246 (p90) REVERT: A 516 LYS cc_start: 0.8020 (pptt) cc_final: 0.7790 (ptmm) REVERT: A 570 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6397 (t0) REVERT: A 657 SER cc_start: 0.8644 (t) cc_final: 0.8396 (m) REVERT: A 663 SER cc_start: 0.8676 (t) cc_final: 0.8196 (p) REVERT: B 58 VAL cc_start: 0.8358 (p) cc_final: 0.8091 (m) REVERT: B 270 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8252 (t80) REVERT: B 688 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7167 (m-80) outliers start: 22 outliers final: 17 residues processed: 203 average time/residue: 0.3346 time to fit residues: 102.5412 Evaluate side-chains 203 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 219 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 139 optimal weight: 0.5980 chunk 201 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN A 117 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072265 restraints weight = 55162.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071378 restraints weight = 57926.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.072163 restraints weight = 51874.179| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18308 Z= 0.109 Angle : 0.502 10.038 24855 Z= 0.264 Chirality : 0.041 0.185 2804 Planarity : 0.003 0.048 3121 Dihedral : 6.460 62.608 2751 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.12 % Allowed : 12.73 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2227 helix: 2.23 (0.17), residues: 875 sheet: -0.44 (0.26), residues: 382 loop : -0.83 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 PHE 0.038 0.001 PHE A 789 TYR 0.013 0.001 TYR B 421 ARG 0.007 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 6) link_NAG-ASN : angle 1.60909 ( 18) link_BETA1-4 : bond 0.00248 ( 3) link_BETA1-4 : angle 1.34588 ( 9) hydrogen bonds : bond 0.04465 ( 760) hydrogen bonds : angle 3.81491 ( 2197) SS BOND : bond 0.00142 ( 18) SS BOND : angle 1.37727 ( 36) covalent geometry : bond 0.00242 (18281) covalent geometry : angle 0.49754 (24792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8375 (tptt) cc_final: 0.7675 (ttpp) REVERT: C 290 TYR cc_start: 0.6520 (p90) cc_final: 0.6279 (p90) REVERT: A 570 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6450 (t0) REVERT: A 657 SER cc_start: 0.8664 (t) cc_final: 0.8422 (m) REVERT: A 663 SER cc_start: 0.8685 (t) cc_final: 0.8189 (p) REVERT: B 58 VAL cc_start: 0.8334 (p) cc_final: 0.8065 (m) REVERT: B 688 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7199 (m-80) outliers start: 21 outliers final: 18 residues processed: 196 average time/residue: 0.3286 time to fit residues: 96.5578 Evaluate side-chains 201 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 73 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073343 restraints weight = 58525.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.073137 restraints weight = 68721.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.073853 restraints weight = 55709.416| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18308 Z= 0.125 Angle : 0.505 9.545 24855 Z= 0.267 Chirality : 0.042 0.184 2804 Planarity : 0.004 0.048 3121 Dihedral : 6.441 61.232 2751 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.18 % Allowed : 12.79 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2227 helix: 2.21 (0.17), residues: 876 sheet: -0.44 (0.26), residues: 382 loop : -0.86 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 PHE 0.039 0.001 PHE A 789 TYR 0.013 0.001 TYR B 421 ARG 0.007 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 6) link_NAG-ASN : angle 1.62782 ( 18) link_BETA1-4 : bond 0.00171 ( 3) link_BETA1-4 : angle 1.39124 ( 9) hydrogen bonds : bond 0.04631 ( 760) hydrogen bonds : angle 3.81034 ( 2197) SS BOND : bond 0.00158 ( 18) SS BOND : angle 1.40512 ( 36) covalent geometry : bond 0.00288 (18281) covalent geometry : angle 0.50054 (24792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8324 (tptt) cc_final: 0.7684 (ttpp) REVERT: C 290 TYR cc_start: 0.6499 (p90) cc_final: 0.6209 (p90) REVERT: A 570 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6432 (t0) REVERT: A 657 SER cc_start: 0.8656 (t) cc_final: 0.8410 (m) REVERT: A 663 SER cc_start: 0.8675 (t) cc_final: 0.8190 (p) REVERT: B 58 VAL cc_start: 0.8359 (p) cc_final: 0.8091 (m) REVERT: B 688 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7180 (m-80) outliers start: 22 outliers final: 20 residues processed: 200 average time/residue: 0.3230 time to fit residues: 96.8904 Evaluate side-chains 205 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 1007 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 26 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 chunk 96 optimal weight: 0.9980 overall best weight: 0.6296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072188 restraints weight = 67538.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072900 restraints weight = 79448.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075032 restraints weight = 52411.832| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18308 Z= 0.114 Angle : 0.501 9.486 24855 Z= 0.263 Chirality : 0.041 0.180 2804 Planarity : 0.003 0.048 3121 Dihedral : 6.356 60.516 2751 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.23 % Allowed : 12.68 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2227 helix: 2.25 (0.17), residues: 872 sheet: -0.42 (0.26), residues: 382 loop : -0.84 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 PHE 0.038 0.001 PHE A 789 TYR 0.013 0.001 TYR B 421 ARG 0.007 0.000 ARG B 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 6) link_NAG-ASN : angle 1.62351 ( 18) link_BETA1-4 : bond 0.00225 ( 3) link_BETA1-4 : angle 1.35391 ( 9) hydrogen bonds : bond 0.04508 ( 760) hydrogen bonds : angle 3.79424 ( 2197) SS BOND : bond 0.00147 ( 18) SS BOND : angle 1.37720 ( 36) covalent geometry : bond 0.00257 (18281) covalent geometry : angle 0.49590 (24792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6258.07 seconds wall clock time: 109 minutes 10.84 seconds (6550.84 seconds total)