Starting phenix.real_space_refine on Wed Jan 15 05:36:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh2_43232/01_2025/8vh2_43232_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh2_43232/01_2025/8vh2_43232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vh2_43232/01_2025/8vh2_43232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh2_43232/01_2025/8vh2_43232.map" model { file = "/net/cci-nas-00/data/ceres_data/8vh2_43232/01_2025/8vh2_43232_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh2_43232/01_2025/8vh2_43232_neut.cif" } resolution = 4.31 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= 0.003 sd= 0.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5430 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 141 5.16 5 C 14664 2.51 5 N 4047 2.21 5 O 4461 1.98 5 H 22914 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 46227 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6959 Classifications: {'peptide': 443} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 421} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3310 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3220 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6959 Classifications: {'peptide': 443} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 421} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3310 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "H" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3220 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "I" Number of atoms: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6959 Classifications: {'peptide': 443} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 421} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3310 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "L" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3220 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Time building chain proxies: 16.20, per 1000 atoms: 0.35 Number of scatterers: 46227 At special positions: 0 Unit cell: (171.72, 191.16, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 O 4461 8.00 N 4047 7.00 C 14664 6.00 H 22914 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5574 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 52 sheets defined 17.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.920A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.651A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 removed outlier: 4.400A pdb=" N ASN A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 574 through 596 removed outlier: 3.705A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.735A pdb=" N TRP B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.513A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 658 removed outlier: 3.843A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.688A pdb=" N THR C 87 " --> pdb=" O TYR C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.728A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.691A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 479 removed outlier: 4.174A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 Processing helix chain 'F' and resid 539 through 543 Processing helix chain 'F' and resid 575 through 593 removed outlier: 4.473A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 removed outlier: 3.694A pdb=" N TRP F 614 " --> pdb=" O ASN F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 626 through 658 removed outlier: 4.146A pdb=" N GLN F 630 " --> pdb=" O MET F 626 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.599A pdb=" N THR G 87 " --> pdb=" O TYR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 186 through 190 Processing helix chain 'G' and resid 212 through 215 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 182 through 189 Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.917A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS I 105 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 195 through 198 removed outlier: 3.508A pdb=" N THR I 198 " --> pdb=" O ASN I 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 195 through 198' Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 373' Processing helix chain 'I' and resid 473 through 479 removed outlier: 4.217A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 535 Processing helix chain 'J' and resid 536 through 541 removed outlier: 4.202A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 596 removed outlier: 4.461A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J 580 " --> pdb=" O LEU J 576 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU J 592 " --> pdb=" O ARG J 588 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU J 593 " --> pdb=" O ASP J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 removed outlier: 3.888A pdb=" N TRP J 614 " --> pdb=" O ASN J 611 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 625 Processing helix chain 'J' and resid 626 through 658 removed outlier: 4.233A pdb=" N GLN J 630 " --> pdb=" O MET J 626 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN J 640 " --> pdb=" O SER J 636 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE J 641 " --> pdb=" O ASN J 637 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR J 643 " --> pdb=" O THR J 639 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN J 653 " --> pdb=" O SER J 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.689A pdb=" N THR K 87 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 186 through 190 removed outlier: 4.211A pdb=" N GLY K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 186 through 190' Processing helix chain 'K' and resid 212 through 215 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 182 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 3.649A pdb=" N GLY A 493 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.616A pdb=" N LYS A 488 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.803A pdb=" N HIS A 216 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.329A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.519A pdb=" N TYR A 191 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 162 removed outlier: 3.605A pdb=" N PHE A 159 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.562A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 261 current: chain 'A' and resid 284 through 309 removed outlier: 7.107A pdb=" N ASN A 301 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 305 " --> pdb=" O ALA A 319 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 463 through 468 Processing sheet with id=AA9, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.616A pdb=" N ALA C 5 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.605A pdb=" N GLY C 10 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 110 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 37 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 38 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 46 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 135 through 145 current: chain 'C' and resid 176 through 185 Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 13 current: chain 'D' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 54 current: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.660A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.589A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 495 through 497 removed outlier: 5.718A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.844A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL E 245 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.636A pdb=" N HIS E 216 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.286A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC5, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.575A pdb=" N PHE E 159 " --> pdb=" O LYS E 172 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 172 " --> pdb=" O PHE E 159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.544A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 261 current: chain 'E' and resid 284 through 309 removed outlier: 7.078A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 305 " --> pdb=" O ALA E 319 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 463 through 468 Processing sheet with id=AC8, first strand: chain 'E' and resid 377 through 378 Processing sheet with id=AC9, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.668A pdb=" N ALA G 5 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 50 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 135 through 145 current: chain 'G' and resid 176 through 185 Processing sheet with id=AD3, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 13 current: chain 'H' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 54 current: chain 'H' and resid 97 through 98 Processing sheet with id=AD6, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.701A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.633A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 495 through 497 removed outlier: 5.920A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.880A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL I 245 " --> pdb=" O ILE I 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 53 through 55 removed outlier: 4.183A pdb=" N HIS I 216 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.286A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AE4, first strand: chain 'I' and resid 143 through 144 Processing sheet with id=AE5, first strand: chain 'I' and resid 159 through 162 removed outlier: 3.859A pdb=" N PHE I 159 " --> pdb=" O LYS I 172 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS I 172 " --> pdb=" O PHE I 159 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.765A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'I' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 261 current: chain 'I' and resid 284 through 309 removed outlier: 7.150A pdb=" N ASN I 301 " --> pdb=" O VAL I 322 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 463 through 468 Processing sheet with id=AE8, first strand: chain 'I' and resid 377 through 378 Processing sheet with id=AE9, first strand: chain 'K' and resid 5 through 8 removed outlier: 3.594A pdb=" N ALA K 5 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER K 21 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET K 80 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR K 70 " --> pdb=" O TYR K 79 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.597A pdb=" N GLY K 10 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE K 110 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN K 95 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR K 33 " --> pdb=" O ASN K 95 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG K 38 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 135 through 145 current: chain 'K' and resid 176 through 185 Processing sheet with id=AF3, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 removed outlier: 3.523A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.742A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.638A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1416 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: 14.23 Time building geometry restraints manager: 11.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22905 1.03 - 1.23: 140 1.23 - 1.43: 9889 1.43 - 1.62: 13593 1.62 - 1.82: 189 Bond restraints: 46716 Sorted by residual: bond pdb=" CA LEU F 587 " pdb=" C LEU F 587 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.41e-02 5.03e+03 5.43e+00 bond pdb=" N GLU A 32 " pdb=" CA GLU A 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU E 32 " pdb=" CA GLU E 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLU I 32 " pdb=" CA GLU I 32 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N VAL B 518 " pdb=" CA VAL B 518 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 46711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 80850 1.31 - 2.62: 3036 2.62 - 3.92: 246 3.92 - 5.23: 44 5.23 - 6.54: 10 Bond angle restraints: 84186 Sorted by residual: angle pdb=" N THR I 132 " pdb=" CA THR I 132 " pdb=" C THR I 132 " ideal model delta sigma weight residual 113.43 107.84 5.59 1.26e+00 6.30e-01 1.97e+01 angle pdb=" C ARG D 30 " pdb=" CA ARG D 30 " pdb=" CB ARG D 30 " ideal model delta sigma weight residual 115.89 110.86 5.03 1.32e+00 5.74e-01 1.45e+01 angle pdb=" C ASN E 461 " pdb=" CA ASN E 461 " pdb=" CB ASN E 461 " ideal model delta sigma weight residual 116.34 111.17 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" N GLU C 65 " pdb=" CA GLU C 65 " pdb=" C GLU C 65 " ideal model delta sigma weight residual 114.62 110.43 4.19 1.14e+00 7.69e-01 1.35e+01 angle pdb=" N THR A 132 " pdb=" CA THR A 132 " pdb=" C THR A 132 " ideal model delta sigma weight residual 112.72 108.25 4.47 1.28e+00 6.10e-01 1.22e+01 ... (remaining 84181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 20235 17.86 - 35.72: 1366 35.72 - 53.58: 429 53.58 - 71.44: 149 71.44 - 89.30: 63 Dihedral angle restraints: 22242 sinusoidal: 12111 harmonic: 10131 Sorted by residual: dihedral pdb=" CB CYS I 499 " pdb=" SG CYS I 499 " pdb=" SG CYS J 605 " pdb=" CB CYS J 605 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS E 499 " pdb=" SG CYS E 499 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -164.90 78.90 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS A 499 " pdb=" SG CYS A 499 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -141.14 55.14 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 22239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2475 0.034 - 0.068: 742 0.068 - 0.101: 221 0.101 - 0.135: 185 0.135 - 0.169: 13 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CA VAL I 42 " pdb=" N VAL I 42 " pdb=" C VAL I 42 " pdb=" CB VAL I 42 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA ILE C 34 " pdb=" N ILE C 34 " pdb=" C ILE C 34 " pdb=" CB ILE C 34 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ILE I 213 " pdb=" N ILE I 213 " pdb=" C ILE I 213 " pdb=" CB ILE I 213 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 3633 not shown) Planarity restraints: 6960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 495 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 496 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 496 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 496 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 75 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO A 76 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 75 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO I 76 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " 0.021 5.00e-02 4.00e+02 ... (remaining 6957 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 987 2.09 - 2.72: 77611 2.72 - 3.35: 124000 3.35 - 3.97: 151628 3.97 - 4.60: 239536 Nonbonded interactions: 593762 Sorted by model distance: nonbonded pdb=" OD1 ASP K 52 " pdb=" H ALA K 53 " model vdw 1.465 2.450 nonbonded pdb=" OD1 ASP G 52 " pdb=" H ALA G 53 " model vdw 1.475 2.450 nonbonded pdb="HH12 ARG K 38 " pdb=" OD1 ASP K 86 " model vdw 1.506 2.450 nonbonded pdb=" OD1 ASP C 52 " pdb=" H ALA C 53 " model vdw 1.513 2.450 nonbonded pdb="HH12 ARG G 38 " pdb=" OD1 ASP G 86 " model vdw 1.524 2.450 ... (remaining 593757 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.610 Extract box with map and model: 1.250 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 70.000 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.160 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:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 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 : 0.003 0.033 23802 Z= 0.208 Angle : 0.640 6.539 32307 Z= 0.377 Chirality : 0.043 0.169 3636 Planarity : 0.004 0.046 4134 Dihedral : 13.282 89.301 8658 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.82 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -1.98 (0.15), residues: 2928 helix: -0.36 (0.27), residues: 378 sheet: -1.08 (0.16), residues: 885 loop : -1.68 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 628 HIS 0.015 0.001 HIS E 374 PHE 0.016 0.001 PHE E 353 TYR 0.020 0.001 TYR G 33 ARG 0.003 0.000 ARG I 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 939 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 THR cc_start: 0.8131 (m) cc_final: 0.7503 (m) REVERT: B 601 LYS cc_start: 0.7575 (mttp) cc_final: 0.6928 (mtmt) REVERT: B 638 TYR cc_start: 0.7593 (m-80) cc_final: 0.7138 (m-80) REVERT: B 639 THR cc_start: 0.8539 (p) cc_final: 0.8303 (t) REVERT: C 52 ASP cc_start: 0.7219 (t0) cc_final: 0.6171 (m-30) REVERT: C 87 THR cc_start: 0.8007 (m) cc_final: 0.7566 (t) REVERT: C 89 MET cc_start: 0.6568 (tpp) cc_final: 0.6298 (ttt) REVERT: C 122 PHE cc_start: 0.8055 (m-80) cc_final: 0.7534 (m-80) REVERT: D 202 SER cc_start: 0.8310 (p) cc_final: 0.8081 (t) REVERT: E 95 MET cc_start: 0.8476 (ppp) cc_final: 0.8254 (ppp) REVERT: E 321 GLN cc_start: 0.7040 (tp40) cc_final: 0.6542 (tm-30) REVERT: F 650 GLN cc_start: 0.8644 (tp40) cc_final: 0.8141 (tp40) REVERT: G 54 ASN cc_start: 0.8471 (p0) cc_final: 0.8258 (p0) REVERT: G 73 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7476 (mtmm) REVERT: G 111 VAL cc_start: 0.8959 (t) cc_final: 0.8478 (t) REVERT: H 73 LEU cc_start: 0.7965 (tp) cc_final: 0.7722 (tt) REVERT: H 91 TYR cc_start: 0.7372 (p90) cc_final: 0.6815 (p90) REVERT: H 151 ASP cc_start: 0.5129 (m-30) cc_final: 0.4518 (m-30) REVERT: H 158 ASN cc_start: 0.7332 (p0) cc_final: 0.6888 (p0) REVERT: H 167 ASP cc_start: 0.7331 (t0) cc_final: 0.7127 (t70) REVERT: H 179 LEU cc_start: 0.9307 (tp) cc_final: 0.8973 (tp) REVERT: H 192 TYR cc_start: 0.7542 (m-80) cc_final: 0.7095 (m-80) REVERT: I 39 TYR cc_start: 0.7966 (m-80) cc_final: 0.7686 (m-80) REVERT: I 95 MET cc_start: 0.8557 (ppp) cc_final: 0.8233 (tmm) REVERT: I 103 GLN cc_start: 0.8640 (mt0) cc_final: 0.8075 (tm-30) REVERT: I 229 ASN cc_start: 0.7018 (m-40) cc_final: 0.6723 (t0) REVERT: I 396 MET cc_start: 0.4507 (mtt) cc_final: 0.4294 (mtt) REVERT: I 464 GLU cc_start: 0.7500 (tp30) cc_final: 0.7284 (tt0) REVERT: J 648 GLU cc_start: 0.8249 (tp30) cc_final: 0.7541 (tm-30) REVERT: K 63 LEU cc_start: 0.8300 (mt) cc_final: 0.8043 (mp) REVERT: K 100 LEU cc_start: 0.7424 (mt) cc_final: 0.6849 (mt) REVERT: K 154 TRP cc_start: 0.7776 (m100) cc_final: 0.7323 (m100) REVERT: K 195 ILE cc_start: 0.7661 (mt) cc_final: 0.7336 (mp) REVERT: L 151 ASP cc_start: 0.6412 (m-30) cc_final: 0.6103 (m-30) outliers start: 0 outliers final: 0 residues processed: 939 average time/residue: 0.7306 time to fit residues: 1021.1399 Evaluate side-chains 569 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 476 ASN B 543 ASN B 640 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN C 102 HIS D 137 ASN D 138 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN G 171 GLN I 249 HIS I 258 GLN I 422 GLN J 651 ASN K 100DHIS K 199 ASN L 138 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.187020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149676 restraints weight = 123559.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158201 restraints weight = 155861.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159443 restraints weight = 56853.536| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 23802 Z= 0.568 Angle : 0.870 8.721 32307 Z= 0.473 Chirality : 0.051 0.246 3636 Planarity : 0.007 0.070 4134 Dihedral : 6.941 32.412 3222 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.48 % Favored : 88.35 % Rotamer: Outliers : 0.19 % Allowed : 6.76 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.14), residues: 2928 helix: -1.00 (0.24), residues: 393 sheet: -1.35 (0.17), residues: 801 loop : -2.43 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 36 HIS 0.011 0.002 HIS C 102 PHE 0.027 0.003 PHE I 317 TYR 0.031 0.003 TYR G 50 ARG 0.009 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 642 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8949 (pttt) cc_final: 0.8597 (ptpp) REVERT: A 106 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 145 MET cc_start: 0.3388 (ttm) cc_final: 0.2965 (ttm) REVERT: A 254 VAL cc_start: 0.8870 (t) cc_final: 0.8575 (p) REVERT: A 473 MET cc_start: 0.8591 (mmm) cc_final: 0.8268 (mmm) REVERT: B 601 LYS cc_start: 0.8018 (mttp) cc_final: 0.7734 (mttm) REVERT: B 622 ILE cc_start: 0.5341 (mt) cc_final: 0.4805 (mt) REVERT: B 634 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8249 (mm-30) REVERT: C 70 TYR cc_start: 0.7966 (p90) cc_final: 0.7718 (p90) REVERT: C 76 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7735 (mp0) REVERT: C 89 MET cc_start: 0.7605 (tpp) cc_final: 0.6922 (ttt) REVERT: C 164 HIS cc_start: 0.6930 (m170) cc_final: 0.6721 (m170) REVERT: C 175 LEU cc_start: 0.8903 (mt) cc_final: 0.8570 (mt) REVERT: D 58 VAL cc_start: 0.7838 (t) cc_final: 0.7545 (t) REVERT: E 103 GLN cc_start: 0.8330 (mt0) cc_final: 0.7809 (mp10) REVERT: E 127 VAL cc_start: 0.9317 (m) cc_final: 0.9106 (m) REVERT: E 161 ILE cc_start: 0.8826 (tp) cc_final: 0.8565 (pt) REVERT: E 321 GLN cc_start: 0.7116 (tp40) cc_final: 0.6640 (tm-30) REVERT: E 359 THR cc_start: 0.9051 (m) cc_final: 0.8849 (p) REVERT: E 429 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7798 (mt-10) REVERT: F 584 GLU cc_start: 0.8344 (pp20) cc_final: 0.7936 (pp20) REVERT: F 626 MET cc_start: 0.7752 (ptp) cc_final: 0.7105 (mtp) REVERT: G 7 TYR cc_start: 0.8577 (m-10) cc_final: 0.8338 (m-10) REVERT: G 54 ASN cc_start: 0.9254 (p0) cc_final: 0.8998 (p0) REVERT: G 85 ASP cc_start: 0.7801 (p0) cc_final: 0.6917 (t70) REVERT: G 113 SER cc_start: 0.8683 (m) cc_final: 0.8349 (p) REVERT: G 144 ASP cc_start: 0.8679 (m-30) cc_final: 0.8200 (m-30) REVERT: G 170 LEU cc_start: 0.8842 (tp) cc_final: 0.8172 (tt) REVERT: H 31 ASN cc_start: 0.7654 (t0) cc_final: 0.7314 (t0) REVERT: H 47 LEU cc_start: 0.8648 (mt) cc_final: 0.8436 (mt) REVERT: H 185 ASP cc_start: 0.7719 (m-30) cc_final: 0.7391 (m-30) REVERT: I 100 MET cc_start: 0.7093 (ptm) cc_final: 0.6869 (ptm) REVERT: I 103 GLN cc_start: 0.8741 (mt0) cc_final: 0.8067 (tm-30) REVERT: I 344 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6721 (mtp180) REVERT: I 396 MET cc_start: 0.6717 (mtt) cc_final: 0.6498 (mtt) REVERT: J 535 MET cc_start: 0.7469 (mmp) cc_final: 0.7244 (mmm) REVERT: J 648 GLU cc_start: 0.8464 (tp30) cc_final: 0.7880 (tm-30) REVERT: K 70 TYR cc_start: 0.8173 (p90) cc_final: 0.7938 (p90) REVERT: K 154 TRP cc_start: 0.7091 (m100) cc_final: 0.6838 (m100) REVERT: L 159 SER cc_start: 0.8810 (p) cc_final: 0.8345 (p) REVERT: L 186 TYR cc_start: 0.6693 (t80) cc_final: 0.6086 (t80) outliers start: 5 outliers final: 3 residues processed: 645 average time/residue: 0.6677 time to fit residues: 651.5635 Evaluate side-chains 488 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 485 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 45 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 276 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 55 optimal weight: 0.0970 chunk 277 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 543 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS D 138 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 543 ASN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 HIS H 137 ASN H 138 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154398 restraints weight = 122717.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.163266 restraints weight = 122921.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163477 restraints weight = 52436.253| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23802 Z= 0.216 Angle : 0.612 6.533 32307 Z= 0.328 Chirality : 0.044 0.168 3636 Planarity : 0.005 0.048 4134 Dihedral : 5.970 28.680 3222 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.24 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.38 (0.14), residues: 2928 helix: -0.46 (0.25), residues: 393 sheet: -1.09 (0.17), residues: 852 loop : -2.19 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 614 HIS 0.006 0.001 HIS C 102 PHE 0.013 0.001 PHE L 116 TYR 0.017 0.001 TYR K 50 ARG 0.005 0.001 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8896 (pttt) cc_final: 0.8593 (ptpp) REVERT: A 106 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 145 MET cc_start: 0.2693 (ttm) cc_final: 0.2363 (ttp) REVERT: A 473 MET cc_start: 0.8437 (mmm) cc_final: 0.8224 (mmm) REVERT: B 601 LYS cc_start: 0.8024 (mttp) cc_final: 0.7714 (mttm) REVERT: B 625 ASN cc_start: 0.7615 (m-40) cc_final: 0.7233 (t0) REVERT: B 626 MET cc_start: 0.6145 (ptp) cc_final: 0.5175 (ptp) REVERT: B 634 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8349 (mm-30) REVERT: C 70 TYR cc_start: 0.7803 (p90) cc_final: 0.7584 (p90) REVERT: C 76 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7690 (mp0) REVERT: C 89 MET cc_start: 0.7425 (tpp) cc_final: 0.7223 (ttt) REVERT: E 95 MET cc_start: 0.8988 (ppp) cc_final: 0.8754 (ppp) REVERT: E 100 MET cc_start: 0.6408 (pmm) cc_final: 0.5563 (pmm) REVERT: E 103 GLN cc_start: 0.8151 (mt0) cc_final: 0.7577 (mp10) REVERT: E 161 ILE cc_start: 0.8769 (tp) cc_final: 0.8532 (pt) REVERT: E 209 SER cc_start: 0.8631 (t) cc_final: 0.8428 (p) REVERT: E 284 ILE cc_start: 0.8761 (mt) cc_final: 0.8557 (mt) REVERT: E 321 GLN cc_start: 0.6919 (tp40) cc_final: 0.6400 (tm-30) REVERT: E 429 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7840 (mt-10) REVERT: F 584 GLU cc_start: 0.8397 (pp20) cc_final: 0.8105 (pp20) REVERT: F 640 GLN cc_start: 0.7756 (pm20) cc_final: 0.6883 (tm-30) REVERT: G 3 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7778 (ttp80) REVERT: G 76 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8293 (mt-10) REVERT: G 85 ASP cc_start: 0.7774 (p0) cc_final: 0.7015 (t70) REVERT: H 31 ASN cc_start: 0.7664 (t0) cc_final: 0.7260 (t0) REVERT: H 88 CYS cc_start: 0.7009 (p) cc_final: 0.6113 (p) REVERT: H 185 ASP cc_start: 0.7802 (m-30) cc_final: 0.7299 (m-30) REVERT: I 100 MET cc_start: 0.6527 (ptm) cc_final: 0.5947 (ppp) REVERT: I 103 GLN cc_start: 0.8656 (mt0) cc_final: 0.8038 (tm-30) REVERT: I 114 GLN cc_start: 0.6643 (tm-30) cc_final: 0.6365 (tp40) REVERT: I 396 MET cc_start: 0.6785 (mtt) cc_final: 0.6561 (mtt) REVERT: I 434 MET cc_start: 0.8601 (ttm) cc_final: 0.8319 (ttp) REVERT: J 648 GLU cc_start: 0.8449 (tp30) cc_final: 0.7810 (tm-30) REVERT: K 70 TYR cc_start: 0.7813 (p90) cc_final: 0.7563 (p90) REVERT: K 76 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7259 (mp0) REVERT: K 154 TRP cc_start: 0.7094 (m100) cc_final: 0.6792 (m100) REVERT: L 96 TRP cc_start: 0.7992 (m100) cc_final: 0.7569 (m100) REVERT: L 186 TYR cc_start: 0.6815 (t80) cc_final: 0.6174 (t80) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.6779 time to fit residues: 639.3207 Evaluate side-chains 483 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 282 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 188 optimal weight: 0.0070 chunk 109 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN G 171 GLN K 39 GLN K 171 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.191609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154162 restraints weight = 122493.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.161416 restraints weight = 135928.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161530 restraints weight = 67374.509| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23802 Z= 0.211 Angle : 0.578 6.046 32307 Z= 0.309 Chirality : 0.043 0.170 3636 Planarity : 0.004 0.046 4134 Dihedral : 5.610 26.184 3222 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.81 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.22 (0.14), residues: 2928 helix: -0.19 (0.26), residues: 393 sheet: -0.84 (0.17), residues: 798 loop : -2.18 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 36 HIS 0.007 0.001 HIS C 102 PHE 0.019 0.001 PHE H 71 TYR 0.014 0.001 TYR K 50 ARG 0.007 0.000 ARG I 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8888 (pttt) cc_final: 0.8676 (ptpp) REVERT: A 106 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8443 (tm-30) REVERT: A 145 MET cc_start: 0.3176 (ttm) cc_final: 0.2787 (ttp) REVERT: A 396 MET cc_start: 0.6184 (mtt) cc_final: 0.5824 (mtt) REVERT: A 473 MET cc_start: 0.8465 (mmm) cc_final: 0.8252 (mmm) REVERT: B 601 LYS cc_start: 0.8139 (mttp) cc_final: 0.7675 (mtpt) REVERT: B 625 ASN cc_start: 0.7520 (m-40) cc_final: 0.7097 (t0) REVERT: B 626 MET cc_start: 0.6226 (ptp) cc_final: 0.5243 (ptp) REVERT: B 634 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8411 (mm-30) REVERT: C 76 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7566 (mp0) REVERT: C 89 MET cc_start: 0.7753 (tpp) cc_final: 0.7527 (ttt) REVERT: D 161 GLU cc_start: 0.8226 (pt0) cc_final: 0.7866 (pm20) REVERT: D 187 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7183 (pp20) REVERT: E 95 MET cc_start: 0.9031 (ppp) cc_final: 0.8767 (ppp) REVERT: E 100 MET cc_start: 0.6004 (pmm) cc_final: 0.5277 (pmm) REVERT: E 103 GLN cc_start: 0.8227 (mt0) cc_final: 0.7742 (mp10) REVERT: E 161 ILE cc_start: 0.8731 (tp) cc_final: 0.8496 (pt) REVERT: E 321 GLN cc_start: 0.6910 (tp40) cc_final: 0.6342 (tm-30) REVERT: E 482 TYR cc_start: 0.8222 (p90) cc_final: 0.8014 (p90) REVERT: F 584 GLU cc_start: 0.8263 (pp20) cc_final: 0.8049 (pp20) REVERT: F 618 ASN cc_start: 0.8528 (t0) cc_final: 0.7980 (t0) REVERT: F 622 ILE cc_start: 0.6917 (mt) cc_final: 0.5819 (mt) REVERT: F 626 MET cc_start: 0.7353 (ptp) cc_final: 0.7089 (mtp) REVERT: F 630 GLN cc_start: 0.7887 (mp10) cc_final: 0.7665 (tp-100) REVERT: F 640 GLN cc_start: 0.7773 (pm20) cc_final: 0.6942 (tm-30) REVERT: G 3 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7765 (ttp80) REVERT: G 6 GLN cc_start: 0.8216 (mt0) cc_final: 0.7864 (mt0) REVERT: G 7 TYR cc_start: 0.8045 (m-10) cc_final: 0.7829 (m-10) REVERT: G 85 ASP cc_start: 0.7667 (p0) cc_final: 0.6907 (t70) REVERT: H 31 ASN cc_start: 0.7488 (t0) cc_final: 0.7194 (t0) REVERT: H 88 CYS cc_start: 0.6794 (p) cc_final: 0.6517 (p) REVERT: H 189 HIS cc_start: 0.6493 (m-70) cc_final: 0.6136 (m-70) REVERT: I 100 MET cc_start: 0.6528 (ptm) cc_final: 0.6018 (ppp) REVERT: I 103 GLN cc_start: 0.8618 (mt0) cc_final: 0.7816 (tm-30) REVERT: I 359 THR cc_start: 0.8805 (t) cc_final: 0.8500 (t) REVERT: J 574 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6637 (pptt) REVERT: J 648 GLU cc_start: 0.8391 (tp30) cc_final: 0.7874 (tm-30) REVERT: K 70 TYR cc_start: 0.7772 (p90) cc_final: 0.7470 (p90) REVERT: K 154 TRP cc_start: 0.7093 (m100) cc_final: 0.6819 (m100) REVERT: K 175 LEU cc_start: 0.8990 (mp) cc_final: 0.8556 (mp) REVERT: L 53 THR cc_start: 0.9146 (m) cc_final: 0.8840 (p) REVERT: L 96 TRP cc_start: 0.8053 (m100) cc_final: 0.7289 (m100) REVERT: L 186 TYR cc_start: 0.6764 (t80) cc_final: 0.6105 (t80) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.6415 time to fit residues: 596.3506 Evaluate side-chains 470 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 223 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 279 optimal weight: 0.4980 chunk 295 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN J 652 GLN K 171 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.192240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.155761 restraints weight = 122850.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163148 restraints weight = 145189.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163375 restraints weight = 70262.143| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 23802 Z= 0.313 Angle : 0.622 8.444 32307 Z= 0.333 Chirality : 0.044 0.174 3636 Planarity : 0.005 0.072 4134 Dihedral : 5.746 27.791 3222 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.38 % Favored : 89.45 % Rotamer: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.32 (0.15), residues: 2928 helix: -0.18 (0.26), residues: 396 sheet: -1.04 (0.18), residues: 810 loop : -2.20 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 96 HIS 0.006 0.001 HIS E 374 PHE 0.021 0.002 PHE H 71 TYR 0.023 0.002 TYR G 33 ARG 0.010 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 567 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8965 (pttt) cc_final: 0.8718 (ptpp) REVERT: A 106 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 601 LYS cc_start: 0.8335 (mttp) cc_final: 0.7942 (mtpt) REVERT: B 634 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 76 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7481 (mp0) REVERT: C 175 LEU cc_start: 0.8722 (mm) cc_final: 0.8485 (mm) REVERT: D 166 GLN cc_start: 0.6809 (pm20) cc_final: 0.6606 (pm20) REVERT: D 187 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7051 (pp20) REVERT: D 197 THR cc_start: 0.7818 (m) cc_final: 0.7547 (p) REVERT: E 95 MET cc_start: 0.9088 (ppp) cc_final: 0.8888 (ppp) REVERT: E 100 MET cc_start: 0.6382 (pmm) cc_final: 0.5415 (pmm) REVERT: E 103 GLN cc_start: 0.8392 (mt0) cc_final: 0.7908 (mp10) REVERT: E 321 GLN cc_start: 0.7076 (tp40) cc_final: 0.6558 (tm-30) REVERT: F 622 ILE cc_start: 0.5810 (mt) cc_final: 0.5521 (mt) REVERT: F 626 MET cc_start: 0.7327 (ptp) cc_final: 0.6827 (mtt) REVERT: F 640 GLN cc_start: 0.7932 (pm20) cc_final: 0.7055 (tm-30) REVERT: G 3 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7762 (ttp80) REVERT: G 85 ASP cc_start: 0.7805 (p0) cc_final: 0.7079 (t70) REVERT: H 31 ASN cc_start: 0.7374 (t0) cc_final: 0.7061 (t0) REVERT: H 43 SER cc_start: 0.9060 (m) cc_final: 0.8855 (p) REVERT: H 189 HIS cc_start: 0.6640 (m-70) cc_final: 0.6208 (m-70) REVERT: I 95 MET cc_start: 0.8654 (ppp) cc_final: 0.8444 (ppp) REVERT: I 116 LEU cc_start: 0.9345 (tp) cc_final: 0.9111 (tt) REVERT: J 648 GLU cc_start: 0.8434 (tp30) cc_final: 0.7885 (tm-30) REVERT: L 53 THR cc_start: 0.9269 (m) cc_final: 0.8944 (p) REVERT: L 186 TYR cc_start: 0.6665 (t80) cc_final: 0.6053 (t80) outliers start: 1 outliers final: 1 residues processed: 568 average time/residue: 0.6331 time to fit residues: 555.4704 Evaluate side-chains 455 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 454 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 108 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 155 optimal weight: 0.3980 chunk 273 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS D 92 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.192744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156271 restraints weight = 123594.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.163847 restraints weight = 140961.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164364 restraints weight = 64754.565| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.7720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23802 Z= 0.201 Angle : 0.565 6.953 32307 Z= 0.300 Chirality : 0.043 0.167 3636 Planarity : 0.004 0.048 4134 Dihedral : 5.416 25.827 3222 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.04 (0.15), residues: 2928 helix: 0.11 (0.26), residues: 405 sheet: -0.58 (0.19), residues: 732 loop : -2.16 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 614 HIS 0.005 0.001 HIS G 100D PHE 0.013 0.001 PHE D 71 TYR 0.015 0.001 TYR C 50 ARG 0.004 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 581 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8929 (pttt) cc_final: 0.8685 (ptpp) REVERT: A 84 MET cc_start: 0.7316 (mpp) cc_final: 0.7077 (mpp) REVERT: A 95 MET cc_start: 0.8876 (ppp) cc_final: 0.8539 (tmm) REVERT: A 106 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 145 MET cc_start: 0.2741 (ttm) cc_final: 0.2229 (ttp) REVERT: B 601 LYS cc_start: 0.8429 (mttp) cc_final: 0.7926 (mtpt) REVERT: B 634 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8388 (mm-30) REVERT: B 639 THR cc_start: 0.7683 (t) cc_final: 0.7452 (t) REVERT: C 175 LEU cc_start: 0.8803 (mm) cc_final: 0.8475 (mm) REVERT: D 42 GLN cc_start: 0.7904 (tt0) cc_final: 0.7492 (mt0) REVERT: D 187 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7072 (pp20) REVERT: D 197 THR cc_start: 0.7741 (m) cc_final: 0.7449 (p) REVERT: E 100 MET cc_start: 0.6264 (pmm) cc_final: 0.5346 (pmm) REVERT: E 103 GLN cc_start: 0.8328 (mt0) cc_final: 0.7721 (mp10) REVERT: E 321 GLN cc_start: 0.6961 (tp40) cc_final: 0.6414 (tm-30) REVERT: F 640 GLN cc_start: 0.7866 (pm20) cc_final: 0.7006 (tm-30) REVERT: G 3 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7772 (ttp80) REVERT: G 7 TYR cc_start: 0.8290 (m-10) cc_final: 0.7971 (m-10) REVERT: G 85 ASP cc_start: 0.7886 (p0) cc_final: 0.7626 (p0) REVERT: H 31 ASN cc_start: 0.7456 (t0) cc_final: 0.7065 (t0) REVERT: H 189 HIS cc_start: 0.6558 (m-70) cc_final: 0.6022 (m-70) REVERT: I 116 LEU cc_start: 0.9314 (tp) cc_final: 0.9020 (tt) REVERT: I 178 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7789 (ttmt) REVERT: I 341 THR cc_start: 0.9425 (p) cc_final: 0.9113 (t) REVERT: K 148 GLU cc_start: 0.8711 (pm20) cc_final: 0.8419 (pm20) REVERT: L 53 THR cc_start: 0.9188 (m) cc_final: 0.8790 (p) REVERT: L 186 TYR cc_start: 0.6781 (t80) cc_final: 0.6134 (t80) outliers start: 1 outliers final: 0 residues processed: 581 average time/residue: 0.6098 time to fit residues: 551.6092 Evaluate side-chains 466 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 112 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 chunk 222 optimal weight: 4.9990 chunk 288 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 273 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN D 92 ASN E 258 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 HIS J 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.190876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145725 restraints weight = 122569.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147001 restraints weight = 81157.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149559 restraints weight = 62050.519| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.8111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23802 Z= 0.319 Angle : 0.620 5.898 32307 Z= 0.333 Chirality : 0.044 0.170 3636 Planarity : 0.005 0.064 4134 Dihedral : 5.644 25.641 3222 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.27 % Favored : 88.56 % Rotamer: Outliers : 0.08 % Allowed : 1.50 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.27 (0.15), residues: 2928 helix: -0.01 (0.26), residues: 405 sheet: -0.97 (0.18), residues: 834 loop : -2.26 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 477 HIS 0.007 0.001 HIS G 35 PHE 0.019 0.002 PHE H 71 TYR 0.025 0.002 TYR K 33 ARG 0.015 0.001 ARG E 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 546 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9004 (pttt) cc_final: 0.8696 (ptpp) REVERT: A 95 MET cc_start: 0.9039 (ppp) cc_final: 0.8606 (tmm) REVERT: A 106 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8350 (tm-30) REVERT: B 601 LYS cc_start: 0.8536 (mttp) cc_final: 0.8037 (mtpt) REVERT: B 626 MET cc_start: 0.6033 (ptp) cc_final: 0.5012 (ptt) REVERT: B 634 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8608 (mm-30) REVERT: C 58 ASP cc_start: 0.9038 (t0) cc_final: 0.8812 (t0) REVERT: C 76 GLU cc_start: 0.7967 (mp0) cc_final: 0.7677 (mp0) REVERT: C 175 LEU cc_start: 0.8910 (mm) cc_final: 0.8466 (mm) REVERT: D 187 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7235 (pp20) REVERT: D 197 THR cc_start: 0.7783 (m) cc_final: 0.7439 (p) REVERT: E 95 MET cc_start: 0.9115 (ppp) cc_final: 0.8859 (ppp) REVERT: E 100 MET cc_start: 0.6288 (pmm) cc_final: 0.5397 (pmm) REVERT: E 103 GLN cc_start: 0.8518 (mt0) cc_final: 0.7850 (mp10) REVERT: E 321 GLN cc_start: 0.7271 (tp40) cc_final: 0.6718 (tm-30) REVERT: F 640 GLN cc_start: 0.7971 (pm20) cc_final: 0.7243 (tm-30) REVERT: G 3 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7736 (ttp80) REVERT: G 6 GLN cc_start: 0.8562 (mt0) cc_final: 0.8165 (mt0) REVERT: G 7 TYR cc_start: 0.8490 (m-10) cc_final: 0.8213 (m-10) REVERT: H 31 ASN cc_start: 0.7360 (t0) cc_final: 0.6948 (t0) REVERT: H 189 HIS cc_start: 0.6817 (m-70) cc_final: 0.6164 (m-70) REVERT: I 116 LEU cc_start: 0.9404 (tp) cc_final: 0.9130 (tt) REVERT: I 178 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7875 (ttmt) REVERT: I 341 THR cc_start: 0.9510 (p) cc_final: 0.9227 (t) REVERT: L 53 THR cc_start: 0.9143 (m) cc_final: 0.8760 (p) outliers start: 2 outliers final: 0 residues processed: 548 average time/residue: 0.6248 time to fit residues: 534.2034 Evaluate side-chains 455 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 9.9990 chunk 264 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 253 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 206 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN D 166 GLN E 258 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN H 138 ASN J 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.192377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153963 restraints weight = 122614.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161279 restraints weight = 134573.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161847 restraints weight = 66198.553| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.8287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23802 Z= 0.173 Angle : 0.554 6.549 32307 Z= 0.293 Chirality : 0.043 0.165 3636 Planarity : 0.004 0.062 4134 Dihedral : 5.262 24.342 3222 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.48 % Favored : 92.38 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -1.97 (0.15), residues: 2928 helix: 0.22 (0.26), residues: 405 sheet: -0.57 (0.19), residues: 774 loop : -2.13 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 112 HIS 0.014 0.001 HIS E 374 PHE 0.015 0.001 PHE E 376 TYR 0.016 0.001 TYR K 91 ARG 0.010 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 554 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8980 (pttt) cc_final: 0.8697 (ptpp) REVERT: A 106 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8380 (tm-30) REVERT: B 601 LYS cc_start: 0.8537 (mttp) cc_final: 0.8038 (mtpt) REVERT: B 634 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8351 (mm-30) REVERT: B 639 THR cc_start: 0.7999 (t) cc_final: 0.7261 (t) REVERT: C 100 LEU cc_start: 0.6907 (mp) cc_final: 0.6687 (mt) REVERT: D 42 GLN cc_start: 0.8020 (tt0) cc_final: 0.7659 (mt0) REVERT: D 106 ILE cc_start: 0.7389 (mp) cc_final: 0.7185 (mt) REVERT: D 139 PHE cc_start: 0.7838 (p90) cc_final: 0.7401 (p90) REVERT: D 161 GLU cc_start: 0.8342 (pm20) cc_final: 0.8042 (tt0) REVERT: D 187 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7148 (pp20) REVERT: D 197 THR cc_start: 0.7763 (m) cc_final: 0.7429 (p) REVERT: E 95 MET cc_start: 0.9068 (ppp) cc_final: 0.8793 (ppp) REVERT: E 100 MET cc_start: 0.6249 (pmm) cc_final: 0.5507 (pmm) REVERT: E 103 GLN cc_start: 0.8444 (mt0) cc_final: 0.7739 (mp10) REVERT: E 321 GLN cc_start: 0.7064 (tp40) cc_final: 0.6510 (tm-30) REVERT: F 534 SER cc_start: 0.9208 (m) cc_final: 0.8765 (p) REVERT: F 640 GLN cc_start: 0.7913 (pm20) cc_final: 0.7225 (tm-30) REVERT: G 3 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7705 (ttp80) REVERT: G 6 GLN cc_start: 0.8088 (mt0) cc_final: 0.7773 (mt0) REVERT: G 7 TYR cc_start: 0.8329 (m-10) cc_final: 0.8093 (m-10) REVERT: G 146 PHE cc_start: 0.8987 (t80) cc_final: 0.8547 (t80) REVERT: H 31 ASN cc_start: 0.7313 (t0) cc_final: 0.6940 (t0) REVERT: H 189 HIS cc_start: 0.6891 (m-70) cc_final: 0.6324 (m-70) REVERT: I 91 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7939 (tm-30) REVERT: I 100 MET cc_start: 0.6350 (ptm) cc_final: 0.6088 (ppp) REVERT: I 103 GLN cc_start: 0.8580 (mt0) cc_final: 0.7778 (tm-30) REVERT: I 178 LYS cc_start: 0.8272 (ptpp) cc_final: 0.8006 (ttmt) REVERT: K 76 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7585 (mp0) REVERT: K 148 GLU cc_start: 0.8770 (pm20) cc_final: 0.8296 (pm20) REVERT: L 53 THR cc_start: 0.9095 (m) cc_final: 0.8659 (p) outliers start: 1 outliers final: 0 residues processed: 555 average time/residue: 0.6367 time to fit residues: 560.5485 Evaluate side-chains 455 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 90 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 199 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 229 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN D 166 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.193493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155470 restraints weight = 117936.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163780 restraints weight = 123569.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.163993 restraints weight = 56140.701| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.8450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23802 Z= 0.195 Angle : 0.554 7.497 32307 Z= 0.293 Chirality : 0.043 0.166 3636 Planarity : 0.004 0.053 4134 Dihedral : 5.178 25.229 3222 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.88 % Favored : 90.98 % Rotamer: Outliers : 0.04 % Allowed : 0.27 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -1.94 (0.15), residues: 2928 helix: 0.19 (0.26), residues: 405 sheet: -0.65 (0.18), residues: 813 loop : -2.06 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP K 154 HIS 0.012 0.001 HIS E 374 PHE 0.016 0.001 PHE C 146 TYR 0.018 0.001 TYR D 173 ARG 0.008 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 537 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8972 (pttt) cc_final: 0.8683 (ptpp) REVERT: A 95 MET cc_start: 0.8769 (ppp) cc_final: 0.8534 (tmm) REVERT: A 106 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 145 MET cc_start: 0.3028 (ttm) cc_final: 0.2378 (ttp) REVERT: B 601 LYS cc_start: 0.8583 (mttp) cc_final: 0.8031 (mtpt) REVERT: B 626 MET cc_start: 0.6629 (ptt) cc_final: 0.5911 (ptt) REVERT: B 634 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8493 (mm-30) REVERT: B 639 THR cc_start: 0.8042 (t) cc_final: 0.7381 (t) REVERT: C 18 MET cc_start: 0.8183 (tmm) cc_final: 0.7949 (tmm) REVERT: C 76 GLU cc_start: 0.8097 (mp0) cc_final: 0.7643 (mp0) REVERT: D 42 GLN cc_start: 0.7998 (tt0) cc_final: 0.7710 (mt0) REVERT: D 161 GLU cc_start: 0.8288 (pm20) cc_final: 0.8033 (tt0) REVERT: D 187 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7077 (pp20) REVERT: D 197 THR cc_start: 0.7765 (m) cc_final: 0.7458 (p) REVERT: E 95 MET cc_start: 0.9085 (ppp) cc_final: 0.8814 (ppp) REVERT: E 100 MET cc_start: 0.6357 (pmm) cc_final: 0.5635 (pmm) REVERT: E 103 GLN cc_start: 0.8459 (mt0) cc_final: 0.7755 (mp10) REVERT: E 211 ASP cc_start: 0.6361 (m-30) cc_final: 0.5759 (p0) REVERT: E 321 GLN cc_start: 0.7042 (tp40) cc_final: 0.6496 (tm-30) REVERT: F 534 SER cc_start: 0.9197 (m) cc_final: 0.8770 (p) REVERT: F 640 GLN cc_start: 0.7926 (pm20) cc_final: 0.7194 (tm-30) REVERT: G 3 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7749 (ttp80) REVERT: G 6 GLN cc_start: 0.8078 (mt0) cc_final: 0.7856 (mt0) REVERT: H 173 TYR cc_start: 0.8713 (m-80) cc_final: 0.8191 (m-10) REVERT: H 189 HIS cc_start: 0.6874 (m-70) cc_final: 0.6193 (m-70) REVERT: I 106 GLU cc_start: 0.8700 (tt0) cc_final: 0.8195 (tm-30) REVERT: I 178 LYS cc_start: 0.8326 (ptpp) cc_final: 0.8006 (ttmt) REVERT: I 341 THR cc_start: 0.9470 (p) cc_final: 0.9167 (t) REVERT: I 434 MET cc_start: 0.8710 (ttp) cc_final: 0.8469 (mtp) REVERT: K 76 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7632 (mp0) REVERT: L 53 THR cc_start: 0.9086 (m) cc_final: 0.8676 (p) outliers start: 1 outliers final: 0 residues processed: 538 average time/residue: 0.6250 time to fit residues: 527.5308 Evaluate side-chains 444 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 89 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150763 restraints weight = 116704.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155341 restraints weight = 109658.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157206 restraints weight = 65055.083| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.8784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 23802 Z= 0.403 Angle : 0.675 7.317 32307 Z= 0.361 Chirality : 0.045 0.193 3636 Planarity : 0.005 0.059 4134 Dihedral : 5.778 26.636 3222 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.77 % Favored : 87.06 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.36 (0.15), residues: 2928 helix: -0.30 (0.26), residues: 402 sheet: -0.81 (0.19), residues: 717 loop : -2.31 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 477 HIS 0.011 0.001 HIS G 100D PHE 0.023 0.002 PHE A 376 TYR 0.034 0.003 TYR C 33 ARG 0.007 0.001 ARG C 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 524 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8964 (pttt) cc_final: 0.8761 (ptpt) REVERT: A 106 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 113 ASP cc_start: 0.8809 (t70) cc_final: 0.8585 (t0) REVERT: A 344 ARG cc_start: 0.7566 (mtp180) cc_final: 0.7304 (mtt180) REVERT: A 368 ASP cc_start: 0.6165 (m-30) cc_final: 0.5879 (m-30) REVERT: B 601 LYS cc_start: 0.8753 (mttp) cc_final: 0.8216 (mtpt) REVERT: B 626 MET cc_start: 0.6753 (ptt) cc_final: 0.5901 (ptt) REVERT: B 634 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8560 (mm-30) REVERT: B 639 THR cc_start: 0.8234 (t) cc_final: 0.7967 (t) REVERT: C 58 ASP cc_start: 0.9223 (t0) cc_final: 0.8915 (t0) REVERT: C 89 MET cc_start: 0.7867 (ttt) cc_final: 0.7548 (mtp) REVERT: D 137 ASN cc_start: 0.8422 (t0) cc_final: 0.8182 (t0) REVERT: D 139 PHE cc_start: 0.7802 (p90) cc_final: 0.7387 (p90) REVERT: D 187 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7219 (pp20) REVERT: D 197 THR cc_start: 0.7847 (m) cc_final: 0.7503 (p) REVERT: E 51 THR cc_start: 0.8605 (m) cc_final: 0.8233 (p) REVERT: E 100 MET cc_start: 0.6320 (pmm) cc_final: 0.5316 (pmm) REVERT: E 103 GLN cc_start: 0.8625 (mt0) cc_final: 0.8050 (mp10) REVERT: E 104 MET cc_start: 0.8358 (tpp) cc_final: 0.7657 (tpp) REVERT: E 145 MET cc_start: 0.4321 (mtp) cc_final: 0.3450 (mtp) REVERT: E 267 GLU cc_start: 0.6971 (tp30) cc_final: 0.6724 (tp30) REVERT: E 321 GLN cc_start: 0.7375 (tp40) cc_final: 0.6835 (tm-30) REVERT: F 584 GLU cc_start: 0.8345 (pp20) cc_final: 0.8081 (pp20) REVERT: G 3 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7882 (ttp80) REVERT: G 85 ASP cc_start: 0.7997 (p0) cc_final: 0.7717 (p0) REVERT: H 189 HIS cc_start: 0.7008 (m-70) cc_final: 0.6328 (m-70) REVERT: I 103 GLN cc_start: 0.8782 (mt0) cc_final: 0.7939 (tm-30) REVERT: I 178 LYS cc_start: 0.8339 (ptpp) cc_final: 0.7984 (ttmt) REVERT: I 213 ILE cc_start: 0.7431 (mt) cc_final: 0.7190 (tt) REVERT: I 368 ASP cc_start: 0.6477 (m-30) cc_final: 0.6247 (m-30) REVERT: J 590 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7753 (tm-30) REVERT: K 76 GLU cc_start: 0.8633 (mt-10) cc_final: 0.7647 (mp0) REVERT: K 175 LEU cc_start: 0.9277 (mp) cc_final: 0.9070 (mp) REVERT: L 53 THR cc_start: 0.9081 (m) cc_final: 0.8786 (p) outliers start: 1 outliers final: 0 residues processed: 525 average time/residue: 0.6280 time to fit residues: 517.8566 Evaluate side-chains 443 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 87 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 216 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 115 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN J 652 GLN K 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.196061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157424 restraints weight = 116489.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163960 restraints weight = 111619.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164196 restraints weight = 63038.787| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.8887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23802 Z= 0.170 Angle : 0.558 6.959 32307 Z= 0.294 Chirality : 0.043 0.165 3636 Planarity : 0.004 0.051 4134 Dihedral : 5.253 26.992 3222 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.48 % Favored : 92.35 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.08 (0.15), residues: 2928 helix: 0.04 (0.26), residues: 405 sheet: -0.78 (0.19), residues: 780 loop : -2.11 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP K 154 HIS 0.006 0.001 HIS G 100D PHE 0.024 0.001 PHE H 71 TYR 0.020 0.001 TYR L 173 ARG 0.008 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11976.62 seconds wall clock time: 206 minutes 5.27 seconds (12365.27 seconds total)