Starting phenix.real_space_refine on Mon Nov 18 23:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/11_2024/8szi_40917.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/11_2024/8szi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/11_2024/8szi_40917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/11_2024/8szi_40917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/11_2024/8szi_40917.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szi_40917/11_2024/8szi_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 15.54, per 1000 atoms: 0.87 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: 4.51 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: 1.98 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: 6.40 Time building geometry restraints manager: 5.18 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 46.620 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.550 ------------------------------------------------------------------------------- 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 18281 Z= 0.482 Angle : 0.966 25.057 24792 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 *********************** 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 : 1.711 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: 0.3310 time to fit residues: 162.9814 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 : 2.003 ------------------------------------------------------------------------------- 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: 0.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 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: 0.2980 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 18281 Z= 0.158 Angle : 0.527 9.347 24792 Z= 0.284 Chirality : 0.042 0.169 2804 Planarity : 0.004 0.046 3121 Dihedral : 8.165 83.361 2751 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.96 % Allowed : 6.31 % Favored : 92.72 % 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: 1.94 (0.18), residues: 877 sheet: -0.45 (0.26), residues: 382 loop : -0.70 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 719 HIS 0.015 0.001 HIS A 766 PHE 0.027 0.001 PHE A 789 TYR 0.013 0.001 TYR B 421 ARG 0.008 0.000 ARG D 197 *********************** 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 235 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7805 (mtm180) REVERT: D 297 TRP cc_start: 0.8319 (m100) cc_final: 0.8063 (m100) REVERT: A 657 SER cc_start: 0.8691 (t) cc_final: 0.8477 (m) REVERT: A 663 SER cc_start: 0.8714 (t) cc_final: 0.8190 (p) REVERT: A 704 LEU cc_start: 0.8365 (tp) cc_final: 0.8062 (mt) REVERT: B 58 VAL cc_start: 0.8276 (p) cc_final: 0.7949 (m) REVERT: B 357 ASN cc_start: 0.8331 (t0) cc_final: 0.7961 (t0) REVERT: B 636 LYS cc_start: 0.6523 (mmtt) cc_final: 0.6314 (mmtt) REVERT: B 643 VAL cc_start: 0.7623 (m) cc_final: 0.7301 (t) REVERT: B 706 PHE cc_start: 0.6097 (t80) cc_final: 0.5759 (t80) REVERT: B 771 MET cc_start: 0.4741 (mmm) cc_final: 0.4484 (mtp) outliers start: 18 outliers final: 9 residues processed: 227 average time/residue: 0.3418 time to fit residues: 115.1356 Evaluate side-chains 202 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 1.973 ------------------------------------------------------------------------------- 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 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 432 GLN B 735 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18281 Z= 0.222 Angle : 0.524 6.689 24792 Z= 0.280 Chirality : 0.043 0.196 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.614 76.477 2751 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.02 % Allowed : 8.35 % Favored : 90.64 % 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: 1.91 (0.17), residues: 886 sheet: -0.51 (0.26), residues: 396 loop : -0.76 (0.19), residues: 945 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 0.020 0.001 PHE B 814 TYR 0.015 0.001 TYR B 421 ARG 0.005 0.000 ARG A 286 *********************** 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 221 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7887 (mtm180) REVERT: A 657 SER cc_start: 0.8677 (t) cc_final: 0.8443 (m) REVERT: A 663 SER cc_start: 0.8732 (t) cc_final: 0.8206 (p) REVERT: A 704 LEU cc_start: 0.8483 (tp) cc_final: 0.8105 (mt) REVERT: B 58 VAL cc_start: 0.8337 (p) cc_final: 0.8023 (m) REVERT: B 643 VAL cc_start: 0.7582 (m) cc_final: 0.7276 (t) REVERT: B 706 PHE cc_start: 0.6134 (t80) cc_final: 0.5758 (t80) REVERT: B 771 MET cc_start: 0.4837 (mmm) cc_final: 0.4491 (mtp) outliers start: 19 outliers final: 13 residues processed: 215 average time/residue: 0.3359 time to fit residues: 107.3327 Evaluate side-chains 202 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 849 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 199 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 309 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 0.038 18281 Z= 0.193 Angle : 0.498 8.563 24792 Z= 0.267 Chirality : 0.042 0.186 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.251 70.968 2751 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.23 % Allowed : 9.79 % Favored : 88.98 % 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: 2.01 (0.17), residues: 882 sheet: -0.52 (0.26), residues: 392 loop : -0.83 (0.19), residues: 953 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 0.025 0.001 PHE A 789 TYR 0.015 0.001 TYR B 421 ARG 0.005 0.000 ARG A 286 *********************** 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 223 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.896 Fit side-chains revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7900 (mtm180) REVERT: D 181 THR cc_start: 0.8164 (p) cc_final: 0.7936 (t) REVERT: A 570 ASP cc_start: 0.6322 (OUTLIER) cc_final: 0.6120 (t0) REVERT: A 657 SER cc_start: 0.8677 (t) cc_final: 0.8453 (m) REVERT: A 663 SER cc_start: 0.8730 (t) cc_final: 0.8197 (p) REVERT: A 716 ARG cc_start: 0.7429 (tpp-160) cc_final: 0.6991 (mmt-90) REVERT: A 789 PHE cc_start: 0.7454 (t80) cc_final: 0.6712 (t80) REVERT: B 58 VAL cc_start: 0.8331 (p) cc_final: 0.8022 (m) REVERT: B 643 VAL cc_start: 0.7535 (m) cc_final: 0.7263 (t) REVERT: B 688 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: B 706 PHE cc_start: 0.6213 (t80) cc_final: 0.5833 (t80) REVERT: B 771 MET cc_start: 0.4653 (mmm) cc_final: 0.4395 (mtp) outliers start: 23 outliers final: 14 residues processed: 215 average time/residue: 0.3371 time to fit residues: 107.9215 Evaluate side-chains 203 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 27 ARG 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 612 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 2.9990 chunk 121 optimal weight: 0.0470 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18281 Z= 0.220 Angle : 0.519 7.918 24792 Z= 0.277 Chirality : 0.043 0.276 2804 Planarity : 0.004 0.048 3121 Dihedral : 7.064 67.798 2751 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.55 % Allowed : 10.17 % Favored : 88.28 % 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: 0.47 (0.18), residues: 2227 helix: 1.98 (0.17), residues: 881 sheet: -0.61 (0.26), residues: 388 loop : -0.86 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 719 HIS 0.012 0.001 HIS A 766 PHE 0.020 0.001 PHE A 789 TYR 0.015 0.001 TYR B 421 ARG 0.006 0.000 ARG B 340 *********************** 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 220 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 2.124 Fit side-chains REVERT: D 181 THR cc_start: 0.8141 (p) cc_final: 0.7926 (t) REVERT: A 570 ASP cc_start: 0.6419 (OUTLIER) cc_final: 0.6199 (t0) REVERT: A 657 SER cc_start: 0.8669 (t) cc_final: 0.8441 (m) REVERT: A 663 SER cc_start: 0.8733 (t) cc_final: 0.8201 (p) REVERT: A 716 ARG cc_start: 0.7471 (tpp-160) cc_final: 0.7013 (mmt-90) REVERT: B 58 VAL cc_start: 0.8340 (p) cc_final: 0.8027 (m) REVERT: B 270 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8249 (t80) REVERT: B 643 VAL cc_start: 0.7518 (m) cc_final: 0.7278 (t) REVERT: B 688 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7206 (m-80) REVERT: B 771 MET cc_start: 0.4656 (mmm) cc_final: 0.4376 (mtp) outliers start: 29 outliers final: 20 residues processed: 210 average time/residue: 0.3222 time to fit residues: 101.8764 Evaluate side-chains 204 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 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 357 ASN 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 618 LEU Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU 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 72 optimal weight: 0.0170 chunk 193 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 214 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18281 Z= 0.172 Angle : 0.496 7.641 24792 Z= 0.265 Chirality : 0.042 0.217 2804 Planarity : 0.004 0.047 3121 Dihedral : 6.854 66.127 2751 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.44 % Allowed : 10.75 % Favored : 87.80 % 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: 2.09 (0.17), residues: 882 sheet: -0.56 (0.26), residues: 386 loop : -0.90 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 99 HIS 0.016 0.001 HIS B 463 PHE 0.024 0.001 PHE A 733 TYR 0.014 0.001 TYR B 421 ARG 0.004 0.000 ARG B 340 *********************** 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 220 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 2.145 Fit side-chains revert: symmetry clash REVERT: A 570 ASP cc_start: 0.6394 (OUTLIER) cc_final: 0.6158 (t0) REVERT: A 657 SER cc_start: 0.8666 (t) cc_final: 0.8441 (m) REVERT: A 663 SER cc_start: 0.8713 (t) cc_final: 0.8189 (p) REVERT: B 58 VAL cc_start: 0.8325 (p) cc_final: 0.8030 (m) REVERT: B 270 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8253 (t80) REVERT: B 688 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: B 771 MET cc_start: 0.4624 (mmm) cc_final: 0.4363 (mtp) REVERT: B 818 TRP cc_start: 0.8398 (m100) cc_final: 0.8120 (m100) outliers start: 27 outliers final: 19 residues processed: 212 average time/residue: 0.3310 time to fit residues: 105.1661 Evaluate side-chains 209 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 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 357 ASN 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 612 PHE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 849 LEU 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 207 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 chunk 180 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18281 Z= 0.168 Angle : 0.491 9.120 24792 Z= 0.260 Chirality : 0.042 0.200 2804 Planarity : 0.003 0.047 3121 Dihedral : 6.640 63.497 2751 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 11.45 % Favored : 87.27 % 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: 0.61 (0.18), residues: 2227 helix: 2.17 (0.17), residues: 882 sheet: -0.52 (0.26), residues: 382 loop : -0.87 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 PHE 0.020 0.001 PHE B 814 TYR 0.013 0.001 TYR B 421 ARG 0.005 0.000 ARG B 340 *********************** 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 219 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.988 Fit side-chains revert: symmetry clash REVERT: A 570 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6248 (t0) REVERT: A 657 SER cc_start: 0.8665 (t) cc_final: 0.8432 (m) REVERT: A 663 SER cc_start: 0.8704 (t) cc_final: 0.8182 (p) REVERT: B 58 VAL cc_start: 0.8335 (p) cc_final: 0.8044 (m) REVERT: B 270 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8203 (t80) REVERT: B 688 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: B 771 MET cc_start: 0.4598 (mmm) cc_final: 0.4343 (mtp) REVERT: B 818 TRP cc_start: 0.8408 (m100) cc_final: 0.8143 (m100) outliers start: 24 outliers final: 18 residues processed: 212 average time/residue: 0.3250 time to fit residues: 103.5351 Evaluate side-chains 206 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 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 357 ASN 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 688 PHE Chi-restraints excluded: chain B residue 849 LEU 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 132 optimal weight: 0.6980 chunk 85 optimal weight: 0.0050 chunk 127 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 168 optimal weight: 0.0770 overall best weight: 0.3752 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18281 Z= 0.136 Angle : 0.477 10.781 24792 Z= 0.253 Chirality : 0.041 0.182 2804 Planarity : 0.003 0.046 3121 Dihedral : 6.487 63.171 2751 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.12 % Allowed : 12.15 % Favored : 86.73 % 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: 0.72 (0.18), residues: 2227 helix: 2.27 (0.17), residues: 877 sheet: -0.45 (0.26), residues: 382 loop : -0.81 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 PHE 0.025 0.001 PHE B 729 TYR 0.012 0.001 TYR B 421 ARG 0.006 0.000 ARG B 340 *********************** 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: 21 poor density : 189 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8361 (tptt) cc_final: 0.7720 (ttpp) REVERT: D 297 TRP cc_start: 0.8287 (m100) cc_final: 0.8022 (m100) REVERT: A 570 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6209 (t0) REVERT: A 657 SER cc_start: 0.8681 (t) cc_final: 0.8453 (m) REVERT: A 663 SER cc_start: 0.8723 (t) cc_final: 0.8205 (p) REVERT: B 58 VAL cc_start: 0.8319 (p) cc_final: 0.8041 (m) REVERT: B 270 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 688 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: B 771 MET cc_start: 0.4556 (mmm) cc_final: 0.4307 (mtp) REVERT: B 818 TRP cc_start: 0.8383 (m100) cc_final: 0.8130 (m100) REVERT: B 819 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8126 (tp) outliers start: 21 outliers final: 13 residues processed: 203 average time/residue: 0.3298 time to fit residues: 99.9273 Evaluate side-chains 203 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 14 LEU 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 570 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 270 PHE 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 819 ILE 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 194 optimal weight: 7.9990 chunk 204 optimal weight: 0.5980 chunk 187 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 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 75 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18281 Z= 0.193 Angle : 0.508 9.509 24792 Z= 0.269 Chirality : 0.042 0.185 2804 Planarity : 0.004 0.048 3121 Dihedral : 6.487 61.243 2751 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.96 % Allowed : 12.79 % Favored : 86.25 % 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: 2.20 (0.17), residues: 876 sheet: -0.46 (0.26), residues: 382 loop : -0.85 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 99 HIS 0.013 0.001 HIS A 766 PHE 0.033 0.001 PHE A 733 TYR 0.013 0.001 TYR B 421 ARG 0.007 0.000 ARG B 340 *********************** 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 205 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: C 29 LYS cc_start: 0.8305 (tptt) cc_final: 0.7671 (ttpp) REVERT: A 570 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.6252 (t0) REVERT: A 657 SER cc_start: 0.8658 (t) cc_final: 0.8427 (m) REVERT: A 663 SER cc_start: 0.8704 (t) cc_final: 0.8188 (p) REVERT: B 58 VAL cc_start: 0.8337 (p) cc_final: 0.8051 (m) REVERT: B 270 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 688 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: B 771 MET cc_start: 0.4614 (mmm) cc_final: 0.4347 (mtp) REVERT: B 818 TRP cc_start: 0.8382 (m100) cc_final: 0.8152 (m100) outliers start: 18 outliers final: 12 residues processed: 199 average time/residue: 0.3349 time to fit residues: 99.3533 Evaluate side-chains 202 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 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 570 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 270 PHE 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 A residue 1007 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 128 optimal weight: 0.0670 chunk 100 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 221 optimal weight: 0.0870 chunk 203 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 136 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18281 Z= 0.131 Angle : 0.478 8.732 24792 Z= 0.253 Chirality : 0.041 0.170 2804 Planarity : 0.003 0.046 3121 Dihedral : 6.257 60.631 2751 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.91 % Allowed : 12.84 % Favored : 86.25 % 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: 0.81 (0.18), residues: 2227 helix: 2.38 (0.17), residues: 870 sheet: -0.43 (0.27), residues: 384 loop : -0.77 (0.19), residues: 973 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 0.024 0.001 PHE B 629 TYR 0.011 0.001 TYR B 421 ARG 0.008 0.000 ARG B 340 ********************** 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 206 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 2.057 Fit side-chains REVERT: C 29 LYS cc_start: 0.8256 (tptt) cc_final: 0.7663 (ttpp) REVERT: D 297 TRP cc_start: 0.8286 (m100) cc_final: 0.8014 (m100) REVERT: A 570 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6172 (t0) REVERT: A 657 SER cc_start: 0.8681 (t) cc_final: 0.8454 (m) REVERT: A 663 SER cc_start: 0.8710 (t) cc_final: 0.8198 (p) REVERT: B 58 VAL cc_start: 0.8280 (p) cc_final: 0.8005 (m) REVERT: B 197 MET cc_start: 0.8279 (mtm) cc_final: 0.7935 (mtt) REVERT: B 688 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: B 771 MET cc_start: 0.4582 (mmm) cc_final: 0.4300 (mtp) REVERT: B 819 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8095 (tp) outliers start: 17 outliers final: 13 residues processed: 202 average time/residue: 0.3435 time to fit residues: 103.2069 Evaluate side-chains 201 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 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 570 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 270 PHE 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 688 PHE Chi-restraints excluded: chain B residue 819 ILE 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 139 optimal weight: 0.3980 chunk 187 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 162 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 176 optimal weight: 0.1980 chunk 73 optimal weight: 0.3980 chunk 181 optimal weight: 0.9980 chunk 22 optimal weight: 0.0270 chunk 32 optimal weight: 0.9990 overall best weight: 0.2638 ------------------------------------------------------------------------------- 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** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.090831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073273 restraints weight = 55288.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.073204 restraints weight = 48442.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073806 restraints weight = 43625.302| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18281 Z= 0.123 Angle : 0.478 8.536 24792 Z= 0.252 Chirality : 0.041 0.167 2804 Planarity : 0.003 0.046 3121 Dihedral : 6.087 59.369 2751 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.96 % Allowed : 12.84 % Favored : 86.20 % 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: 0.87 (0.18), residues: 2227 helix: 2.40 (0.17), residues: 872 sheet: -0.39 (0.27), residues: 384 loop : -0.70 (0.20), residues: 971 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 0.030 0.001 PHE B 729 TYR 0.011 0.001 TYR C 302 ARG 0.007 0.000 ARG B 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3596.96 seconds wall clock time: 66 minutes 51.96 seconds (4011.96 seconds total)