Starting phenix.real_space_refine on Thu Oct 10 09:15:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh2_43232/10_2024/8vh2_43232_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh2_43232/10_2024/8vh2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh2_43232/10_2024/8vh2_43232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh2_43232/10_2024/8vh2_43232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh2_43232/10_2024/8vh2_43232_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh2_43232/10_2024/8vh2_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-5477/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: 16.23, 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: 8.60 Conformation dependent library (CDL) restraints added in 2.6 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: 3.23 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: 13.65 Time building geometry restraints manager: 10.50 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: 0.00 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: 1.010 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: 1.220 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 69.200 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.150 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 939 time to evaluate : 2.716 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: 0.7237 time to fit residues: 1007.9306 Evaluate side-chains 569 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 2.715 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 fitting. rotamer outliers: 5 poor density : 642 time to evaluate : 2.726 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: 0.9010 (pttt) cc_final: 0.8532 (ptpp) REVERT: A 106 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8655 (tm-30) REVERT: A 145 MET cc_start: 0.3375 (ttm) cc_final: 0.2975 (ttm) REVERT: A 172 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7529 (mmtt) REVERT: A 254 VAL cc_start: 0.8888 (t) cc_final: 0.8645 (p) REVERT: A 473 MET cc_start: 0.8400 (mmm) cc_final: 0.7986 (mmm) REVERT: B 601 LYS cc_start: 0.8061 (mttp) cc_final: 0.7728 (mttm) REVERT: B 622 ILE cc_start: 0.5299 (mt) cc_final: 0.4808 (mt) REVERT: B 634 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8332 (mm-30) REVERT: C 76 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7779 (mp0) REVERT: C 89 MET cc_start: 0.8012 (tpp) cc_final: 0.7344 (ttt) REVERT: C 164 HIS cc_start: 0.7459 (m170) cc_final: 0.7174 (m170) REVERT: C 175 LEU cc_start: 0.8987 (mt) cc_final: 0.8709 (mt) REVERT: D 58 VAL cc_start: 0.7654 (t) cc_final: 0.7344 (t) REVERT: E 95 MET cc_start: 0.9120 (ppp) cc_final: 0.8908 (ppp) REVERT: E 103 GLN cc_start: 0.8444 (mt0) cc_final: 0.7783 (mp10) REVERT: E 127 VAL cc_start: 0.9300 (m) cc_final: 0.9049 (m) REVERT: E 161 ILE cc_start: 0.8573 (tp) cc_final: 0.8231 (pt) REVERT: E 321 GLN cc_start: 0.7326 (tp40) cc_final: 0.6811 (tm-30) REVERT: E 359 THR cc_start: 0.9013 (m) cc_final: 0.8799 (p) REVERT: E 429 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7704 (mt-10) REVERT: F 584 GLU cc_start: 0.8247 (pp20) cc_final: 0.7812 (pp20) REVERT: F 626 MET cc_start: 0.7777 (ptp) cc_final: 0.7232 (mtp) REVERT: G 7 TYR cc_start: 0.8573 (m-10) cc_final: 0.8317 (m-10) REVERT: G 85 ASP cc_start: 0.7516 (p0) cc_final: 0.6652 (t70) REVERT: G 113 SER cc_start: 0.8754 (m) cc_final: 0.8416 (p) REVERT: G 144 ASP cc_start: 0.8796 (m-30) cc_final: 0.8292 (m-30) REVERT: G 170 LEU cc_start: 0.9002 (tp) cc_final: 0.8492 (tt) REVERT: H 31 ASN cc_start: 0.7235 (t0) cc_final: 0.6868 (t0) REVERT: H 47 LEU cc_start: 0.8727 (mt) cc_final: 0.8487 (mt) REVERT: H 139 PHE cc_start: 0.8651 (p90) cc_final: 0.8353 (p90) REVERT: H 185 ASP cc_start: 0.8208 (m-30) cc_final: 0.7731 (m-30) REVERT: I 84 MET cc_start: 0.7506 (mpp) cc_final: 0.7294 (mpp) REVERT: I 103 GLN cc_start: 0.8918 (mt0) cc_final: 0.8044 (tm-30) REVERT: I 292 VAL cc_start: 0.9291 (t) cc_final: 0.9089 (p) REVERT: I 344 ARG cc_start: 0.6991 (mtm180) cc_final: 0.6762 (mtp180) REVERT: I 396 MET cc_start: 0.6473 (mtt) cc_final: 0.6258 (mtt) REVERT: J 535 MET cc_start: 0.7562 (mmp) cc_final: 0.7292 (mmm) REVERT: J 648 GLU cc_start: 0.8544 (tp30) cc_final: 0.7998 (tm-30) REVERT: K 154 TRP cc_start: 0.7885 (m100) cc_final: 0.7411 (m100) REVERT: K 195 ILE cc_start: 0.7795 (mt) cc_final: 0.7417 (mp) REVERT: L 159 SER cc_start: 0.8922 (p) cc_final: 0.8404 (p) REVERT: L 186 TYR cc_start: 0.6773 (t80) cc_final: 0.6134 (t80) outliers start: 5 outliers final: 3 residues processed: 645 average time/residue: 0.6953 time to fit residues: 682.8348 Evaluate side-chains 489 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 486 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 0.0970 chunk 224 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 240 optimal weight: 0.0970 chunk 267 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23802 Z= 0.179 Angle : 0.596 6.743 32307 Z= 0.318 Chirality : 0.044 0.166 3636 Planarity : 0.004 0.049 4134 Dihedral : 5.808 28.036 3222 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.11 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -2.25 (0.14), residues: 2928 helix: -0.36 (0.25), residues: 393 sheet: -1.02 (0.17), residues: 846 loop : -2.08 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 614 HIS 0.006 0.001 HIS C 102 PHE 0.015 0.001 PHE L 116 TYR 0.017 0.001 TYR C 70 ARG 0.006 0.000 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 643 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 3.134 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: A 49 LYS cc_start: 0.8830 (pttt) cc_final: 0.8045 (ptpp) REVERT: A 106 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 145 MET cc_start: 0.2842 (ttm) cc_final: 0.2494 (ttp) REVERT: A 194 ILE cc_start: 0.8541 (tp) cc_final: 0.8331 (tp) REVERT: A 473 MET cc_start: 0.8009 (mmm) cc_final: 0.7729 (mmm) REVERT: B 634 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8229 (mm-30) REVERT: C 76 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7857 (mp0) REVERT: C 164 HIS cc_start: 0.7477 (m170) cc_final: 0.7209 (m170) REVERT: D 58 VAL cc_start: 0.7393 (t) cc_final: 0.7183 (t) REVERT: E 95 MET cc_start: 0.8977 (ppp) cc_final: 0.8447 (ppp) REVERT: E 100 MET cc_start: 0.6087 (pmm) cc_final: 0.5270 (pmm) REVERT: E 103 GLN cc_start: 0.8199 (mt0) cc_final: 0.7557 (mp10) REVERT: E 161 ILE cc_start: 0.8512 (tp) cc_final: 0.8233 (pt) REVERT: E 172 LYS cc_start: 0.8251 (mmtt) cc_final: 0.8004 (mmtt) REVERT: E 209 SER cc_start: 0.8575 (t) cc_final: 0.8339 (p) REVERT: E 321 GLN cc_start: 0.7088 (tp40) cc_final: 0.6508 (tm-30) REVERT: E 429 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7418 (mt-10) REVERT: E 482 TYR cc_start: 0.8456 (p90) cc_final: 0.8067 (p90) REVERT: F 584 GLU cc_start: 0.8249 (pp20) cc_final: 0.7945 (pp20) REVERT: F 618 ASN cc_start: 0.8473 (t0) cc_final: 0.8168 (t0) REVERT: F 640 GLN cc_start: 0.7707 (pm20) cc_final: 0.6910 (tm-30) REVERT: G 3 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7700 (ttp80) REVERT: G 6 GLN cc_start: 0.8557 (mt0) cc_final: 0.8247 (mt0) REVERT: G 7 TYR cc_start: 0.8376 (m-10) cc_final: 0.8170 (m-10) REVERT: G 85 ASP cc_start: 0.7396 (p0) cc_final: 0.6693 (t70) REVERT: H 31 ASN cc_start: 0.7163 (t0) cc_final: 0.6716 (t0) REVERT: H 58 VAL cc_start: 0.8428 (t) cc_final: 0.8202 (t) REVERT: H 88 CYS cc_start: 0.7706 (p) cc_final: 0.6898 (p) REVERT: H 139 PHE cc_start: 0.8671 (p90) cc_final: 0.8279 (p90) REVERT: H 185 ASP cc_start: 0.8172 (m-30) cc_final: 0.7533 (m-30) REVERT: H 189 HIS cc_start: 0.7070 (m-70) cc_final: 0.6859 (m-70) REVERT: I 84 MET cc_start: 0.7591 (mpp) cc_final: 0.7370 (mpp) REVERT: I 95 MET cc_start: 0.8614 (ppp) cc_final: 0.8384 (ppp) REVERT: I 100 MET cc_start: 0.6498 (ptm) cc_final: 0.5985 (ppp) REVERT: I 103 GLN cc_start: 0.8720 (mt0) cc_final: 0.7965 (tm-30) REVERT: I 114 GLN cc_start: 0.6570 (tm-30) cc_final: 0.6350 (tp40) REVERT: I 208 VAL cc_start: 0.8286 (m) cc_final: 0.8075 (p) REVERT: I 434 MET cc_start: 0.8349 (ttm) cc_final: 0.8087 (ttp) REVERT: J 648 GLU cc_start: 0.8474 (tp30) cc_final: 0.7787 (tm-30) REVERT: K 6 GLN cc_start: 0.8186 (tt0) cc_final: 0.7790 (tt0) REVERT: K 76 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7325 (mp0) REVERT: K 105 SER cc_start: 0.8700 (p) cc_final: 0.7793 (t) REVERT: K 148 GLU cc_start: 0.8679 (pm20) cc_final: 0.8289 (pm20) REVERT: K 154 TRP cc_start: 0.7746 (m100) cc_final: 0.7154 (m100) REVERT: K 195 ILE cc_start: 0.7784 (mt) cc_final: 0.7365 (mp) REVERT: L 186 TYR cc_start: 0.6830 (t80) cc_final: 0.6202 (t80) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.6614 time to fit residues: 649.3877 Evaluate side-chains 498 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 181 optimal weight: 0.0570 chunk 271 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- 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 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN G 171 GLN I 422 GLN K 39 GLN K 171 GLN L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23802 Z= 0.361 Angle : 0.661 7.205 32307 Z= 0.355 Chirality : 0.045 0.176 3636 Planarity : 0.005 0.064 4134 Dihedral : 5.986 28.699 3222 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.75 % Favored : 88.05 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -2.41 (0.14), residues: 2928 helix: -0.39 (0.25), residues: 396 sheet: -0.98 (0.18), residues: 777 loop : -2.28 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 96 HIS 0.009 0.001 HIS C 102 PHE 0.022 0.002 PHE H 71 TYR 0.024 0.002 TYR K 50 ARG 0.008 0.001 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 595 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 2.788 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: 0.9018 (pttt) cc_final: 0.8720 (ptpp) REVERT: A 95 MET cc_start: 0.8893 (tmm) cc_final: 0.8655 (tmm) REVERT: A 106 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8664 (tm-30) REVERT: A 145 MET cc_start: 0.3099 (ttm) cc_final: 0.2874 (ttp) REVERT: B 601 LYS cc_start: 0.8763 (mttt) cc_final: 0.8495 (mtpt) REVERT: B 626 MET cc_start: 0.6468 (ptp) cc_final: 0.5243 (ptp) REVERT: B 634 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 76 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7681 (mp0) REVERT: C 164 HIS cc_start: 0.7643 (m170) cc_final: 0.7371 (m170) REVERT: D 58 VAL cc_start: 0.7773 (t) cc_final: 0.7537 (t) REVERT: D 187 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7618 (pp20) REVERT: D 197 THR cc_start: 0.7894 (m) cc_final: 0.7563 (p) REVERT: E 95 MET cc_start: 0.9008 (ppp) cc_final: 0.8594 (ppp) REVERT: E 100 MET cc_start: 0.5853 (pmm) cc_final: 0.5030 (pmm) REVERT: E 103 GLN cc_start: 0.8458 (mt0) cc_final: 0.7880 (mp10) REVERT: E 145 MET cc_start: 0.4339 (mtp) cc_final: 0.3478 (mtp) REVERT: E 321 GLN cc_start: 0.7396 (tp40) cc_final: 0.6831 (tm-30) REVERT: E 429 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7745 (mt-10) REVERT: E 434 MET cc_start: 0.7966 (mtm) cc_final: 0.7735 (mtm) REVERT: F 584 GLU cc_start: 0.8307 (pp20) cc_final: 0.8020 (pp20) REVERT: F 622 ILE cc_start: 0.6253 (mt) cc_final: 0.6013 (mt) REVERT: F 626 MET cc_start: 0.7529 (ptp) cc_final: 0.6793 (mtt) REVERT: F 630 GLN cc_start: 0.8164 (mp10) cc_final: 0.7850 (tp-100) REVERT: F 640 GLN cc_start: 0.7862 (pm20) cc_final: 0.6973 (tm-30) REVERT: G 3 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7825 (ttp80) REVERT: G 85 ASP cc_start: 0.7365 (p0) cc_final: 0.6715 (t70) REVERT: H 31 ASN cc_start: 0.6989 (t0) cc_final: 0.6684 (t0) REVERT: H 43 SER cc_start: 0.9147 (m) cc_final: 0.8942 (p) REVERT: H 88 CYS cc_start: 0.7646 (p) cc_final: 0.7295 (p) REVERT: H 185 ASP cc_start: 0.8229 (m-30) cc_final: 0.7770 (m-30) REVERT: I 114 GLN cc_start: 0.6816 (tm-30) cc_final: 0.6568 (tp40) REVERT: I 359 THR cc_start: 0.8846 (t) cc_final: 0.8558 (t) REVERT: I 434 MET cc_start: 0.8500 (ttm) cc_final: 0.8192 (ttp) REVERT: K 154 TRP cc_start: 0.7821 (m100) cc_final: 0.7414 (m100) REVERT: K 195 ILE cc_start: 0.7753 (mt) cc_final: 0.7401 (mp) REVERT: L 17 GLU cc_start: 0.6770 (tt0) cc_final: 0.6354 (tp30) REVERT: L 42 GLN cc_start: 0.7876 (mp10) cc_final: 0.7608 (mp10) REVERT: L 53 THR cc_start: 0.9333 (m) cc_final: 0.9115 (p) REVERT: L 100 GLN cc_start: 0.8425 (mp-120) cc_final: 0.8218 (mm-40) REVERT: L 186 TYR cc_start: 0.6747 (t80) cc_final: 0.6064 (t80) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.6121 time to fit residues: 565.3057 Evaluate side-chains 457 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 198 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 616 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23802 Z= 0.193 Angle : 0.573 5.954 32307 Z= 0.305 Chirality : 0.043 0.168 3636 Planarity : 0.004 0.062 4134 Dihedral : 5.543 26.713 3222 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.56 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -2.01 (0.15), residues: 2928 helix: 0.16 (0.26), residues: 387 sheet: -0.54 (0.18), residues: 753 loop : -2.15 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.007 0.001 HIS A 374 PHE 0.015 0.001 PHE H 98 TYR 0.015 0.001 TYR K 33 ARG 0.007 0.000 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 587 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 2.730 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: A 49 LYS cc_start: 0.9053 (pttt) cc_final: 0.8688 (ptpp) REVERT: A 106 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8646 (tm-30) REVERT: A 145 MET cc_start: 0.2956 (ttm) cc_final: 0.2229 (ttt) REVERT: A 315 GLN cc_start: 0.7823 (mp-120) cc_final: 0.7548 (mp10) REVERT: A 462 ASN cc_start: 0.7660 (t0) cc_final: 0.7404 (t0) REVERT: B 601 LYS cc_start: 0.8771 (mttt) cc_final: 0.8490 (mtpt) REVERT: B 626 MET cc_start: 0.6109 (ptp) cc_final: 0.5342 (ptp) REVERT: B 634 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8410 (mm-30) REVERT: C 164 HIS cc_start: 0.7659 (m170) cc_final: 0.7358 (m170) REVERT: C 175 LEU cc_start: 0.8563 (mt) cc_final: 0.8225 (mp) REVERT: D 58 VAL cc_start: 0.7678 (t) cc_final: 0.7460 (t) REVERT: D 187 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7532 (pp20) REVERT: D 197 THR cc_start: 0.7885 (m) cc_final: 0.7584 (p) REVERT: E 95 MET cc_start: 0.8966 (ppp) cc_final: 0.8497 (ppp) REVERT: E 100 MET cc_start: 0.5974 (pmm) cc_final: 0.5083 (pmm) REVERT: E 103 GLN cc_start: 0.8367 (mt0) cc_final: 0.7765 (mp10) REVERT: E 122 LEU cc_start: 0.9251 (mp) cc_final: 0.8995 (mp) REVERT: E 172 LYS cc_start: 0.8271 (mmtt) cc_final: 0.8002 (mmtt) REVERT: E 321 GLN cc_start: 0.7251 (tp40) cc_final: 0.6632 (tm-30) REVERT: E 429 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7729 (mt-10) REVERT: F 584 GLU cc_start: 0.8266 (pp20) cc_final: 0.7999 (pp20) REVERT: F 622 ILE cc_start: 0.6199 (mt) cc_final: 0.5661 (mt) REVERT: F 626 MET cc_start: 0.7461 (ptp) cc_final: 0.7004 (mtp) REVERT: F 630 GLN cc_start: 0.8040 (mp10) cc_final: 0.7807 (tp-100) REVERT: F 640 GLN cc_start: 0.7776 (pm20) cc_final: 0.6975 (tm-30) REVERT: F 654 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7242 (tp30) REVERT: G 3 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7737 (ttp80) REVERT: G 85 ASP cc_start: 0.7458 (p0) cc_final: 0.6691 (t70) REVERT: H 31 ASN cc_start: 0.6954 (t0) cc_final: 0.6493 (t0) REVERT: H 91 TYR cc_start: 0.7852 (p90) cc_final: 0.7350 (p90) REVERT: H 185 ASP cc_start: 0.8077 (m-30) cc_final: 0.7863 (m-30) REVERT: I 100 MET cc_start: 0.6652 (ptm) cc_final: 0.6060 (ppp) REVERT: I 103 GLN cc_start: 0.8813 (mt0) cc_final: 0.7777 (tm-30) REVERT: I 114 GLN cc_start: 0.6808 (tm-30) cc_final: 0.6524 (tp40) REVERT: I 434 MET cc_start: 0.8444 (ttm) cc_final: 0.8167 (ttp) REVERT: J 626 MET cc_start: 0.7178 (mtm) cc_final: 0.6874 (ptp) REVERT: J 648 GLU cc_start: 0.8401 (tp30) cc_final: 0.7912 (tm-30) REVERT: K 154 TRP cc_start: 0.7805 (m100) cc_final: 0.7265 (m100) REVERT: K 195 ILE cc_start: 0.7732 (mt) cc_final: 0.7377 (mp) REVERT: L 53 THR cc_start: 0.9332 (m) cc_final: 0.9020 (p) REVERT: L 186 TYR cc_start: 0.6822 (t80) cc_final: 0.6082 (t80) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.6378 time to fit residues: 580.4570 Evaluate side-chains 453 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 10.0000 chunk 258 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 168 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN D 166 GLN E 258 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.7814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23802 Z= 0.314 Angle : 0.615 5.821 32307 Z= 0.329 Chirality : 0.044 0.171 3636 Planarity : 0.005 0.055 4134 Dihedral : 5.687 26.971 3222 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.34 % Favored : 88.46 % Rotamer: Outliers : 0.08 % Allowed : 1.65 % 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: -2.25 (0.15), residues: 2928 helix: 0.17 (0.26), residues: 387 sheet: -0.99 (0.18), residues: 816 loop : -2.23 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 614 HIS 0.006 0.001 HIS G 100D PHE 0.019 0.002 PHE H 71 TYR 0.024 0.002 TYR K 33 ARG 0.011 0.001 ARG E 467 *********************** 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 555 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 553 time to evaluate : 2.733 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: 0.9056 (pttt) cc_final: 0.8700 (ptpp) REVERT: A 84 MET cc_start: 0.7280 (mpp) cc_final: 0.6937 (mpp) REVERT: A 106 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8657 (tm-30) REVERT: A 145 MET cc_start: 0.3263 (ttm) cc_final: 0.2462 (ttt) REVERT: A 246 GLN cc_start: 0.8763 (mt0) cc_final: 0.8525 (mt0) REVERT: A 462 ASN cc_start: 0.7617 (t0) cc_final: 0.7392 (t0) REVERT: B 601 LYS cc_start: 0.8871 (mttt) cc_final: 0.8617 (mtpt) REVERT: B 626 MET cc_start: 0.6519 (ptp) cc_final: 0.5282 (ptp) REVERT: B 634 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 639 THR cc_start: 0.7932 (t) cc_final: 0.7690 (t) REVERT: C 76 GLU cc_start: 0.8026 (mp0) cc_final: 0.7679 (mp0) REVERT: C 164 HIS cc_start: 0.7709 (m170) cc_final: 0.7447 (m170) REVERT: D 58 VAL cc_start: 0.7800 (t) cc_final: 0.7490 (t) REVERT: D 187 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7629 (pp20) REVERT: D 197 THR cc_start: 0.7885 (m) cc_final: 0.7553 (p) REVERT: E 95 MET cc_start: 0.8988 (ppp) cc_final: 0.8510 (ppp) REVERT: E 100 MET cc_start: 0.5999 (pmm) cc_final: 0.5137 (pmm) REVERT: E 103 GLN cc_start: 0.8529 (mt0) cc_final: 0.7922 (mp10) REVERT: E 122 LEU cc_start: 0.9218 (mp) cc_final: 0.8979 (mp) REVERT: E 321 GLN cc_start: 0.7382 (tp40) cc_final: 0.6775 (tm-30) REVERT: E 429 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7803 (mt-10) REVERT: F 584 GLU cc_start: 0.8311 (pp20) cc_final: 0.8033 (pp20) REVERT: F 622 ILE cc_start: 0.6299 (mt) cc_final: 0.5729 (mt) REVERT: F 630 GLN cc_start: 0.8093 (mp10) cc_final: 0.7867 (tp-100) REVERT: F 640 GLN cc_start: 0.7974 (pm20) cc_final: 0.7180 (tm-30) REVERT: G 3 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7787 (ttp80) REVERT: G 85 ASP cc_start: 0.7453 (p0) cc_final: 0.7183 (p0) REVERT: H 31 ASN cc_start: 0.6947 (t0) cc_final: 0.6616 (t0) REVERT: H 185 ASP cc_start: 0.8120 (m-30) cc_final: 0.7686 (m-30) REVERT: H 189 HIS cc_start: 0.7209 (m-70) cc_final: 0.6976 (m-70) REVERT: I 434 MET cc_start: 0.8444 (ttm) cc_final: 0.8106 (ttp) REVERT: K 81 ASP cc_start: 0.7439 (m-30) cc_final: 0.7198 (m-30) REVERT: K 89 MET cc_start: 0.7691 (mmm) cc_final: 0.7208 (mtp) REVERT: K 154 TRP cc_start: 0.7893 (m100) cc_final: 0.7479 (m100) REVERT: K 195 ILE cc_start: 0.7778 (mt) cc_final: 0.7438 (mp) REVERT: L 53 THR cc_start: 0.9337 (m) cc_final: 0.9019 (p) REVERT: L 186 TYR cc_start: 0.6937 (t80) cc_final: 0.6221 (t80) outliers start: 2 outliers final: 0 residues processed: 554 average time/residue: 0.6394 time to fit residues: 556.1188 Evaluate side-chains 453 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 241 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 286 optimal weight: 4.9990 chunk 179 optimal weight: 0.0870 chunk 174 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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 171 GLN C 204 ASN E 258 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN G 200 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23802 Z= 0.198 Angle : 0.555 5.720 32307 Z= 0.296 Chirality : 0.043 0.167 3636 Planarity : 0.004 0.047 4134 Dihedral : 5.334 24.859 3222 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.31 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -2.02 (0.15), residues: 2928 helix: 0.36 (0.27), residues: 387 sheet: -0.62 (0.19), residues: 738 loop : -2.16 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 112 HIS 0.010 0.001 HIS E 374 PHE 0.014 0.001 PHE C 146 TYR 0.018 0.001 TYR C 7 ARG 0.005 0.000 ARG G 83 *********************** 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 578 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 2.765 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: A 49 LYS cc_start: 0.8979 (pttt) cc_final: 0.8381 (ptpp) REVERT: A 84 MET cc_start: 0.7258 (mpp) cc_final: 0.6966 (mpp) REVERT: A 106 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 145 MET cc_start: 0.3042 (ttm) cc_final: 0.2286 (ttt) REVERT: A 246 GLN cc_start: 0.8811 (mt0) cc_final: 0.8548 (mt0) REVERT: B 601 LYS cc_start: 0.8841 (mttt) cc_final: 0.8551 (mtpt) REVERT: B 626 MET cc_start: 0.6100 (ptp) cc_final: 0.5315 (ptp) REVERT: B 634 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8257 (mm-30) REVERT: B 639 THR cc_start: 0.7873 (t) cc_final: 0.7605 (t) REVERT: C 76 GLU cc_start: 0.7944 (mp0) cc_final: 0.7565 (mp0) REVERT: C 100 LEU cc_start: 0.7084 (mp) cc_final: 0.6826 (mt) REVERT: D 42 GLN cc_start: 0.8122 (tt0) cc_final: 0.7609 (mt0) REVERT: D 58 VAL cc_start: 0.7883 (t) cc_final: 0.7631 (t) REVERT: D 161 GLU cc_start: 0.8457 (pm20) cc_final: 0.8056 (pm20) REVERT: D 187 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7533 (pp20) REVERT: D 197 THR cc_start: 0.7867 (m) cc_final: 0.7510 (p) REVERT: E 95 MET cc_start: 0.8956 (ppp) cc_final: 0.8492 (ppp) REVERT: E 100 MET cc_start: 0.5896 (pmm) cc_final: 0.5138 (pmm) REVERT: E 103 GLN cc_start: 0.8507 (mt0) cc_final: 0.7803 (mp10) REVERT: E 122 LEU cc_start: 0.9200 (mp) cc_final: 0.8970 (mp) REVERT: E 172 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8072 (mmtt) REVERT: E 297 THR cc_start: 0.8932 (p) cc_final: 0.8711 (t) REVERT: E 321 GLN cc_start: 0.7283 (tp40) cc_final: 0.6668 (tm-30) REVERT: F 534 SER cc_start: 0.9250 (m) cc_final: 0.8798 (p) REVERT: F 584 GLU cc_start: 0.8267 (pp20) cc_final: 0.8037 (pp20) REVERT: F 640 GLN cc_start: 0.7921 (pm20) cc_final: 0.7154 (tm-30) REVERT: G 3 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7739 (ttp80) REVERT: G 6 GLN cc_start: 0.8205 (mt0) cc_final: 0.7953 (mt0) REVERT: G 164 HIS cc_start: 0.7853 (m170) cc_final: 0.7576 (m170) REVERT: H 31 ASN cc_start: 0.6869 (t0) cc_final: 0.6492 (t0) REVERT: H 88 CYS cc_start: 0.7350 (p) cc_final: 0.7066 (p) REVERT: H 185 ASP cc_start: 0.8087 (m-30) cc_final: 0.7761 (m-30) REVERT: I 103 GLN cc_start: 0.8723 (mt0) cc_final: 0.7788 (tm-30) REVERT: I 178 LYS cc_start: 0.8341 (ptpp) cc_final: 0.7878 (ttmt) REVERT: I 246 GLN cc_start: 0.8298 (mt0) cc_final: 0.8085 (mt0) REVERT: I 341 THR cc_start: 0.9471 (p) cc_final: 0.9139 (t) REVERT: I 434 MET cc_start: 0.8380 (ttm) cc_final: 0.8101 (ttp) REVERT: I 462 ASN cc_start: 0.8325 (p0) cc_final: 0.8092 (p0) REVERT: J 601 LYS cc_start: 0.8526 (mttp) cc_final: 0.8318 (mtmm) REVERT: J 626 MET cc_start: 0.7211 (mtm) cc_final: 0.6944 (ptp) REVERT: K 89 MET cc_start: 0.7663 (mmm) cc_final: 0.7207 (mtp) REVERT: K 110 ILE cc_start: 0.8833 (pt) cc_final: 0.8603 (pt) REVERT: K 148 GLU cc_start: 0.9065 (pm20) cc_final: 0.8464 (pm20) REVERT: K 154 TRP cc_start: 0.7950 (m100) cc_final: 0.7517 (m100) REVERT: K 195 ILE cc_start: 0.7776 (mt) cc_final: 0.7419 (mp) REVERT: L 53 THR cc_start: 0.9273 (m) cc_final: 0.8942 (p) REVERT: L 186 TYR cc_start: 0.6944 (t80) cc_final: 0.6215 (t80) outliers start: 0 outliers final: 0 residues processed: 578 average time/residue: 0.6622 time to fit residues: 595.4575 Evaluate side-chains 469 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN J 652 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.8285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23802 Z= 0.257 Angle : 0.581 6.706 32307 Z= 0.309 Chirality : 0.043 0.169 3636 Planarity : 0.004 0.046 4134 Dihedral : 5.417 25.087 3222 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.21 % Favored : 89.62 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.46 % 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: -2.02 (0.15), residues: 2928 helix: 0.53 (0.27), residues: 378 sheet: -0.68 (0.18), residues: 786 loop : -2.19 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 112 HIS 0.006 0.001 HIS G 100D PHE 0.015 0.001 PHE H 71 TYR 0.019 0.002 TYR C 33 ARG 0.005 0.000 ARG C 210 *********************** 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 559 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 558 time to evaluate : 2.722 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: 0.8586 (ptpp) REVERT: A 106 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 145 MET cc_start: 0.3046 (ttm) cc_final: 0.2273 (ttt) REVERT: A 246 GLN cc_start: 0.8802 (mt0) cc_final: 0.8452 (mt0) REVERT: B 601 LYS cc_start: 0.8853 (mttt) cc_final: 0.8581 (mtpt) REVERT: B 626 MET cc_start: 0.6110 (ptp) cc_final: 0.5299 (ptp) REVERT: B 634 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8352 (mm-30) REVERT: B 639 THR cc_start: 0.7909 (t) cc_final: 0.7676 (t) REVERT: C 76 GLU cc_start: 0.8016 (mp0) cc_final: 0.7527 (mp0) REVERT: C 89 MET cc_start: 0.7949 (mtp) cc_final: 0.7740 (mtp) REVERT: D 42 GLN cc_start: 0.8277 (tt0) cc_final: 0.7709 (mt0) REVERT: D 58 VAL cc_start: 0.7919 (t) cc_final: 0.7649 (t) REVERT: D 106 ILE cc_start: 0.7407 (mt) cc_final: 0.7191 (mp) REVERT: D 107 LYS cc_start: 0.8123 (tptt) cc_final: 0.7916 (tppt) REVERT: D 139 PHE cc_start: 0.8018 (p90) cc_final: 0.7426 (p90) REVERT: D 161 GLU cc_start: 0.8491 (pm20) cc_final: 0.8092 (pm20) REVERT: D 185 ASP cc_start: 0.7186 (m-30) cc_final: 0.6974 (m-30) REVERT: D 187 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7385 (pp20) REVERT: D 197 THR cc_start: 0.7841 (m) cc_final: 0.7483 (p) REVERT: E 95 MET cc_start: 0.8972 (ppp) cc_final: 0.8521 (ppp) REVERT: E 100 MET cc_start: 0.6026 (pmm) cc_final: 0.5356 (pmm) REVERT: E 103 GLN cc_start: 0.8572 (mt0) cc_final: 0.7848 (mp10) REVERT: E 122 LEU cc_start: 0.9152 (mp) cc_final: 0.8934 (mp) REVERT: E 321 GLN cc_start: 0.7341 (tp40) cc_final: 0.6737 (tm-30) REVERT: F 534 SER cc_start: 0.9299 (m) cc_final: 0.8857 (p) REVERT: F 584 GLU cc_start: 0.8312 (pp20) cc_final: 0.7990 (pp20) REVERT: F 640 GLN cc_start: 0.7956 (pm20) cc_final: 0.7223 (tm-30) REVERT: G 3 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7748 (ttp80) REVERT: G 6 GLN cc_start: 0.8345 (mt0) cc_final: 0.8034 (mt0) REVERT: G 12 LYS cc_start: 0.9129 (mmtp) cc_final: 0.8853 (mmtm) REVERT: G 85 ASP cc_start: 0.7670 (p0) cc_final: 0.7405 (p0) REVERT: H 185 ASP cc_start: 0.8012 (m-30) cc_final: 0.7760 (m-30) REVERT: I 100 MET cc_start: 0.6658 (ptm) cc_final: 0.6301 (ppp) REVERT: I 178 LYS cc_start: 0.8346 (ptpp) cc_final: 0.7905 (ttmt) REVERT: I 213 ILE cc_start: 0.7275 (mt) cc_final: 0.7054 (tt) REVERT: I 246 GLN cc_start: 0.8349 (mt0) cc_final: 0.8122 (mt0) REVERT: I 341 THR cc_start: 0.9490 (p) cc_final: 0.9210 (t) REVERT: I 434 MET cc_start: 0.8409 (ttm) cc_final: 0.8096 (ttp) REVERT: J 626 MET cc_start: 0.7236 (mtm) cc_final: 0.6971 (ptp) REVERT: K 148 GLU cc_start: 0.8574 (pm20) cc_final: 0.8231 (pm20) REVERT: K 154 TRP cc_start: 0.8021 (m100) cc_final: 0.7593 (m100) REVERT: K 195 ILE cc_start: 0.7803 (mt) cc_final: 0.7434 (mp) REVERT: L 53 THR cc_start: 0.9283 (m) cc_final: 0.8897 (p) REVERT: L 186 TYR cc_start: 0.6952 (t80) cc_final: 0.6189 (t80) outliers start: 1 outliers final: 0 residues processed: 559 average time/residue: 0.6657 time to fit residues: 585.1052 Evaluate side-chains 466 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 160 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 171 GLN E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.8438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23802 Z= 0.162 Angle : 0.538 6.607 32307 Z= 0.283 Chirality : 0.043 0.167 3636 Planarity : 0.004 0.046 4134 Dihedral : 5.073 23.929 3222 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.90 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.85 (0.15), residues: 2928 helix: 0.69 (0.27), residues: 378 sheet: -0.60 (0.19), residues: 762 loop : -2.05 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 36 HIS 0.005 0.001 HIS G 100D PHE 0.014 0.001 PHE A 317 TYR 0.013 0.001 TYR K 91 ARG 0.006 0.000 ARG C 210 *********************** 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 568 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 2.738 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: 0.8940 (pttt) cc_final: 0.8595 (ptpp) REVERT: A 106 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 145 MET cc_start: 0.2849 (ttm) cc_final: 0.2016 (ttt) REVERT: A 246 GLN cc_start: 0.8799 (mt0) cc_final: 0.8280 (mt0) REVERT: B 535 MET cc_start: 0.8103 (mmp) cc_final: 0.7897 (mmp) REVERT: B 601 LYS cc_start: 0.8839 (mttt) cc_final: 0.8570 (mtpt) REVERT: B 625 ASN cc_start: 0.7333 (t0) cc_final: 0.6865 (t0) REVERT: B 626 MET cc_start: 0.6077 (ptp) cc_final: 0.5426 (ptp) REVERT: B 634 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 639 THR cc_start: 0.8008 (t) cc_final: 0.7262 (t) REVERT: C 100 LEU cc_start: 0.7348 (mp) cc_final: 0.7116 (mt) REVERT: D 42 GLN cc_start: 0.8184 (tt0) cc_final: 0.7724 (mt0) REVERT: D 58 VAL cc_start: 0.7818 (t) cc_final: 0.7535 (t) REVERT: D 139 PHE cc_start: 0.7903 (p90) cc_final: 0.7337 (p90) REVERT: D 161 GLU cc_start: 0.8493 (pm20) cc_final: 0.8060 (pm20) REVERT: D 187 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7382 (pp20) REVERT: E 95 MET cc_start: 0.8911 (ppp) cc_final: 0.8457 (ppp) REVERT: E 100 MET cc_start: 0.6045 (pmm) cc_final: 0.5356 (pmm) REVERT: E 103 GLN cc_start: 0.8532 (mt0) cc_final: 0.7799 (mp10) REVERT: E 122 LEU cc_start: 0.9012 (mp) cc_final: 0.8706 (mp) REVERT: E 211 ASP cc_start: 0.6282 (m-30) cc_final: 0.5645 (p0) REVERT: E 321 GLN cc_start: 0.7318 (tp40) cc_final: 0.6660 (tm-30) REVERT: F 534 SER cc_start: 0.9284 (m) cc_final: 0.8905 (p) REVERT: F 584 GLU cc_start: 0.8264 (pp20) cc_final: 0.8012 (pp20) REVERT: F 640 GLN cc_start: 0.7883 (pm20) cc_final: 0.7200 (tm-30) REVERT: G 3 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7678 (ttp80) REVERT: G 85 ASP cc_start: 0.7667 (p0) cc_final: 0.7376 (p0) REVERT: G 209 LYS cc_start: 0.6443 (tptm) cc_final: 0.6014 (tptp) REVERT: H 139 PHE cc_start: 0.8152 (p90) cc_final: 0.7714 (p90) REVERT: H 173 TYR cc_start: 0.8583 (m-80) cc_final: 0.7990 (m-10) REVERT: H 185 ASP cc_start: 0.7962 (m-30) cc_final: 0.7682 (m-30) REVERT: H 189 HIS cc_start: 0.6882 (m-70) cc_final: 0.6253 (m-70) REVERT: I 178 LYS cc_start: 0.8405 (ptpp) cc_final: 0.8027 (ttmt) REVERT: I 341 THR cc_start: 0.9476 (p) cc_final: 0.9228 (t) REVERT: I 434 MET cc_start: 0.8356 (ttm) cc_final: 0.8060 (ttp) REVERT: J 621 GLU cc_start: 0.8005 (pm20) cc_final: 0.7772 (pm20) REVERT: J 626 MET cc_start: 0.7234 (mtm) cc_final: 0.7003 (ptp) REVERT: K 89 MET cc_start: 0.7647 (mmm) cc_final: 0.7163 (mtp) REVERT: K 105 SER cc_start: 0.8681 (p) cc_final: 0.8130 (t) REVERT: K 148 GLU cc_start: 0.8578 (pm20) cc_final: 0.8280 (pm20) REVERT: K 154 TRP cc_start: 0.8010 (m100) cc_final: 0.7596 (m100) REVERT: K 171 GLN cc_start: 0.8624 (mt0) cc_final: 0.8180 (mt0) REVERT: K 175 LEU cc_start: 0.9238 (mp) cc_final: 0.8985 (mp) REVERT: K 195 ILE cc_start: 0.7793 (mt) cc_final: 0.7432 (mp) REVERT: L 53 THR cc_start: 0.9200 (m) cc_final: 0.8776 (p) REVERT: L 186 TYR cc_start: 0.6939 (t80) cc_final: 0.6158 (t80) outliers start: 0 outliers final: 0 residues processed: 568 average time/residue: 0.6396 time to fit residues: 568.5434 Evaluate side-chains 474 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.8677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23802 Z= 0.290 Angle : 0.590 6.340 32307 Z= 0.314 Chirality : 0.043 0.177 3636 Planarity : 0.004 0.045 4134 Dihedral : 5.300 26.111 3222 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.89 % Favored : 88.90 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.50 (0.27), residues: 378 sheet: -0.71 (0.18), residues: 807 loop : -2.14 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 96 HIS 0.008 0.001 HIS G 100D PHE 0.021 0.002 PHE L 71 TYR 0.024 0.002 TYR K 33 ARG 0.006 0.000 ARG C 210 ********************** 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 543 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 2.735 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: A 49 LYS cc_start: 0.9002 (pttt) cc_final: 0.8633 (ptpp) REVERT: A 106 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 145 MET cc_start: 0.3045 (ttm) cc_final: 0.2203 (ttt) REVERT: A 246 GLN cc_start: 0.8832 (mt0) cc_final: 0.8309 (mt0) REVERT: A 344 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7336 (mtp180) REVERT: B 601 LYS cc_start: 0.8888 (mttt) cc_final: 0.8615 (mtpt) REVERT: B 626 MET cc_start: 0.6209 (ptp) cc_final: 0.5299 (ptp) REVERT: B 630 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7835 (tp40) REVERT: B 639 THR cc_start: 0.8163 (t) cc_final: 0.7878 (t) REVERT: D 58 VAL cc_start: 0.7978 (t) cc_final: 0.7710 (t) REVERT: D 106 ILE cc_start: 0.7627 (mp) cc_final: 0.7398 (mp) REVERT: D 137 ASN cc_start: 0.8346 (t0) cc_final: 0.8034 (t0) REVERT: D 139 PHE cc_start: 0.7876 (p90) cc_final: 0.7317 (p90) REVERT: D 149 LYS cc_start: 0.8424 (tttt) cc_final: 0.8192 (ttmm) REVERT: D 161 GLU cc_start: 0.8561 (pm20) cc_final: 0.8131 (pm20) REVERT: D 187 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7491 (pp20) REVERT: D 197 THR cc_start: 0.7874 (m) cc_final: 0.7377 (p) REVERT: E 95 MET cc_start: 0.8956 (ppp) cc_final: 0.8512 (ppp) REVERT: E 100 MET cc_start: 0.6129 (pmm) cc_final: 0.5407 (pmm) REVERT: E 103 GLN cc_start: 0.8649 (mt0) cc_final: 0.7919 (mp10) REVERT: E 104 MET cc_start: 0.8776 (tpp) cc_final: 0.8149 (tpp) REVERT: E 122 LEU cc_start: 0.9016 (mp) cc_final: 0.8662 (mp) REVERT: E 321 GLN cc_start: 0.7436 (tp40) cc_final: 0.6850 (tm-30) REVERT: E 368 ASP cc_start: 0.6479 (m-30) cc_final: 0.6271 (m-30) REVERT: F 534 SER cc_start: 0.9319 (m) cc_final: 0.8966 (p) REVERT: F 584 GLU cc_start: 0.8296 (pp20) cc_final: 0.7962 (pp20) REVERT: G 3 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.7697 (ttp80) REVERT: G 85 ASP cc_start: 0.7726 (p0) cc_final: 0.7448 (p0) REVERT: G 171 GLN cc_start: 0.7856 (mp10) cc_final: 0.7261 (mp10) REVERT: G 209 LYS cc_start: 0.6305 (tptm) cc_final: 0.5930 (tptp) REVERT: H 139 PHE cc_start: 0.8166 (p90) cc_final: 0.7772 (p90) REVERT: H 185 ASP cc_start: 0.7983 (m-30) cc_final: 0.7683 (m-30) REVERT: H 189 HIS cc_start: 0.6870 (m-70) cc_final: 0.6353 (m-70) REVERT: I 103 GLN cc_start: 0.8801 (mt0) cc_final: 0.7857 (tm-30) REVERT: I 106 GLU cc_start: 0.8928 (tt0) cc_final: 0.8328 (tm-30) REVERT: I 178 LYS cc_start: 0.8479 (ptpp) cc_final: 0.8071 (ttmt) REVERT: I 434 MET cc_start: 0.8398 (ttm) cc_final: 0.8112 (ttp) REVERT: J 590 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7917 (tm-30) REVERT: J 626 MET cc_start: 0.7224 (mtm) cc_final: 0.6854 (ptp) REVERT: K 89 MET cc_start: 0.7932 (mmm) cc_final: 0.7729 (mtp) REVERT: K 148 GLU cc_start: 0.8545 (pm20) cc_final: 0.8249 (pm20) REVERT: K 154 TRP cc_start: 0.8060 (m100) cc_final: 0.7583 (m100) REVERT: K 171 GLN cc_start: 0.8761 (mt0) cc_final: 0.8540 (mt0) REVERT: K 175 LEU cc_start: 0.9328 (mp) cc_final: 0.9105 (mp) REVERT: K 195 ILE cc_start: 0.7821 (mt) cc_final: 0.7459 (mp) REVERT: L 53 THR cc_start: 0.9252 (m) cc_final: 0.8845 (p) REVERT: L 187 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8133 (mm-30) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.6047 time to fit residues: 511.7521 Evaluate side-chains 453 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.195318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154967 restraints weight = 116282.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162896 restraints weight = 112404.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162775 restraints weight = 57948.559| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.8808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23802 Z= 0.223 Angle : 0.563 7.424 32307 Z= 0.297 Chirality : 0.043 0.169 3636 Planarity : 0.004 0.045 4134 Dihedral : 5.190 27.058 3222 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.67 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.93 (0.15), residues: 2928 helix: 0.50 (0.27), residues: 381 sheet: -0.66 (0.18), residues: 807 loop : -2.10 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 35 HIS 0.005 0.001 HIS G 100D PHE 0.025 0.001 PHE L 71 TYR 0.023 0.002 TYR G 33 ARG 0.006 0.000 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10087.02 seconds wall clock time: 174 minutes 14.87 seconds (10454.87 seconds total)