Starting phenix.real_space_refine on Tue Feb 20 10:23:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vhy_8687/02_2024/5vhy_8687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vhy_8687/02_2024/5vhy_8687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vhy_8687/02_2024/5vhy_8687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vhy_8687/02_2024/5vhy_8687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vhy_8687/02_2024/5vhy_8687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vhy_8687/02_2024/5vhy_8687_updated.pdb" } resolution = 4.6 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 144 5.16 5 C 17704 2.51 5 N 4558 2.21 5 O 5150 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 660": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 303": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "E ARG 4": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 89": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27572 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6159 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 760} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6137 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6159 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 760} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 6137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6137 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1408 Classifications: {'peptide': 179} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1408 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 174} Chain breaks: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'NAG': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.89, per 1000 atoms: 0.50 Number of scatterers: 27572 At special positions: 0 Unit cell: (121.68, 165.36, 197.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 4 15.00 F 12 9.00 O 5150 8.00 N 4558 7.00 C 17704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 11.00 Conformation dependent library (CDL) restraints added in 4.7 seconds 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 29 sheets defined 45.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.714A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.754A pdb=" N SER A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 280 through 302 removed outlier: 3.587A pdb=" N LYS A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.642A pdb=" N ARG A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 523 through 543 removed outlier: 3.792A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 584 Processing helix chain 'A' and resid 598 through 629 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.667A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.556A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 776 through 781 removed outlier: 4.046A pdb=" N LYS A 781 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 819 removed outlier: 4.757A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.681A pdb=" N ASN B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 143 through 155 removed outlier: 3.555A pdb=" N SER B 152 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.529A pdb=" N LEU B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.700A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.564A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.605A pdb=" N GLU B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 523 through 543 removed outlier: 3.577A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 584 Processing helix chain 'B' and resid 599 through 625 Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.533A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 790 through 816 removed outlier: 4.126A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.752A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 253 through 262 removed outlier: 4.002A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 removed outlier: 3.626A pdb=" N LYS C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.625A pdb=" N GLU C 328 " --> pdb=" O GLN C 325 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 330 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 334 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 523 through 543 removed outlier: 3.565A pdb=" N VAL C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 584 Processing helix chain 'C' and resid 599 through 629 Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.505A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 Processing helix chain 'C' and resid 686 through 694 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 777 through 781 removed outlier: 4.068A pdb=" N LYS C 781 " --> pdb=" O SER C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 819 removed outlier: 3.724A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.928A pdb=" N LYS D 156 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 175 through 187 removed outlier: 3.658A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.741A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.562A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.624A pdb=" N GLU D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 514 through 516 No H-bonds generated for 'chain 'D' and resid 514 through 516' Processing helix chain 'D' and resid 523 through 543 removed outlier: 3.574A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 598 through 625 Processing helix chain 'D' and resid 636 through 641 removed outlier: 3.529A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 694 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 755 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 790 through 816 removed outlier: 4.166A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 Processing helix chain 'E' and resid 119 through 151 Processing helix chain 'E' and resid 159 through 192 removed outlier: 3.704A pdb=" N PHE E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET E 181 " --> pdb=" O MET E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 230 Processing helix chain 'F' and resid 2 through 26 Processing helix chain 'F' and resid 119 through 151 Processing helix chain 'F' and resid 159 through 192 removed outlier: 3.668A pdb=" N PHE F 164 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 230 removed outlier: 3.683A pdb=" N LEU F 211 " --> pdb=" O TRP F 207 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 15 Processing sheet with id= B, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.627A pdb=" N PHE A 133 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS A 364 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= D, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= E, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.004A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.277A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 11 through 17 removed outlier: 6.838A pdb=" N ARG B 42 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE B 14 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N THR B 44 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 16 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N HIS B 46 " --> pdb=" O GLY B 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 134 through 137 removed outlier: 6.228A pdb=" N THR B 161 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR B 137 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE B 163 " --> pdb=" O TYR B 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 191 through 194 removed outlier: 6.470A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 396 through 399 removed outlier: 6.283A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= L, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.810A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 732 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.859A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 11 through 19 removed outlier: 6.536A pdb=" N ARG C 42 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE C 14 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR C 44 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C 16 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS C 46 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE C 18 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP C 48 " --> pdb=" O PHE C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.296A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= Q, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= R, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.023A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.156A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 11 through 17 removed outlier: 6.917A pdb=" N ARG D 42 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE D 14 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR D 44 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY D 16 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS D 46 " --> pdb=" O GLY D 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 96 through 98 Processing sheet with id= V, first strand: chain 'D' and resid 134 through 137 removed outlier: 6.112A pdb=" N THR D 161 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N TYR D 137 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE D 163 " --> pdb=" O TYR D 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 191 through 194 removed outlier: 6.466A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 396 through 399 removed outlier: 6.154A pdb=" N LYS D 441 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR D 399 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR D 443 " --> pdb=" O THR D 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= Z, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.749A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.520A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 89 through 92 Processing sheet with id= AC, first strand: chain 'F' and resid 89 through 92 1154 hydrogen bonds defined for protein. 3312 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: 10.36 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8704 1.35 - 1.48: 7235 1.48 - 1.60: 11981 1.60 - 1.73: 8 1.73 - 1.86: 234 Bond restraints: 28162 Sorted by residual: bond pdb=" CAT ZK1 B1101 " pdb=" OAA ZK1 B1101 " ideal model delta sigma weight residual 1.214 1.407 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" CAT ZK1 C1101 " pdb=" OAA ZK1 C1101 " ideal model delta sigma weight residual 1.214 1.406 -0.192 2.00e-02 2.50e+03 9.26e+01 bond pdb=" CAT ZK1 A1101 " pdb=" OAA ZK1 A1101 " ideal model delta sigma weight residual 1.214 1.406 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" CAT ZK1 D1101 " pdb=" OAA ZK1 D1101 " ideal model delta sigma weight residual 1.214 1.405 -0.191 2.00e-02 2.50e+03 9.14e+01 bond pdb=" CAU ZK1 D1101 " pdb=" OAB ZK1 D1101 " ideal model delta sigma weight residual 1.215 1.402 -0.187 2.00e-02 2.50e+03 8.78e+01 ... (remaining 28157 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.00: 468 106.00 - 113.00: 15315 113.00 - 120.00: 8764 120.00 - 127.01: 13310 127.01 - 134.01: 231 Bond angle restraints: 38088 Sorted by residual: angle pdb=" C THR B 98 " pdb=" N PRO B 99 " pdb=" CA PRO B 99 " ideal model delta sigma weight residual 119.28 128.37 -9.09 1.10e+00 8.26e-01 6.83e+01 angle pdb=" C THR D 98 " pdb=" N PRO D 99 " pdb=" CA PRO D 99 " ideal model delta sigma weight residual 119.28 128.26 -8.98 1.10e+00 8.26e-01 6.66e+01 angle pdb=" C LYS C 511 " pdb=" N PRO C 512 " pdb=" CA PRO C 512 " ideal model delta sigma weight residual 120.03 128.05 -8.02 9.90e-01 1.02e+00 6.56e+01 angle pdb=" C HIS A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta sigma weight residual 119.78 125.63 -5.85 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C HIS C 107 " pdb=" N PRO C 108 " pdb=" CA PRO C 108 " ideal model delta sigma weight residual 119.78 125.35 -5.57 1.03e+00 9.43e-01 2.92e+01 ... (remaining 38083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 16338 16.27 - 32.54: 301 32.54 - 48.82: 96 48.82 - 65.09: 14 65.09 - 81.36: 15 Dihedral angle restraints: 16764 sinusoidal: 6740 harmonic: 10024 Sorted by residual: dihedral pdb=" CA SER A 139 " pdb=" C SER A 139 " pdb=" N ASP A 140 " pdb=" CA ASP A 140 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR A 137 " pdb=" C TYR A 137 " pdb=" N ASP A 138 " pdb=" CA ASP A 138 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN A 318 " pdb=" C ASN A 318 " pdb=" N PRO A 319 " pdb=" CA PRO A 319 " ideal model delta harmonic sigma weight residual 0.00 -17.75 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 16761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2509 0.031 - 0.062: 1103 0.062 - 0.094: 468 0.094 - 0.125: 143 0.125 - 0.156: 13 Chirality restraints: 4236 Sorted by residual: chirality pdb=" CA ASP A 519 " pdb=" N ASP A 519 " pdb=" C ASP A 519 " pdb=" CB ASP A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE E 113 " pdb=" N ILE E 113 " pdb=" C ILE E 113 " pdb=" CB ILE E 113 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE F 113 " pdb=" N ILE F 113 " pdb=" C ILE F 113 " pdb=" CB ILE F 113 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 4233 not shown) Planarity restraints: 4768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO C 99 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.060 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO A 99 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 116 " 0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO E 117 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 117 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 117 " 0.046 5.00e-02 4.00e+02 ... (remaining 4765 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 194 2.44 - 3.06: 20522 3.06 - 3.67: 42840 3.67 - 4.29: 64905 4.29 - 4.90: 98497 Nonbonded interactions: 226958 Sorted by model distance: nonbonded pdb=" O TRP E 31 " pdb=" O GLY E 206 " model vdw 1.831 3.040 nonbonded pdb=" CE2 PHE A 541 " pdb=" CB LEU E 227 " model vdw 1.870 3.740 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.057 2.440 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.076 2.440 nonbonded pdb=" CE2 PHE E 187 " pdb=" NE1 TRP E 203 " model vdw 2.103 3.420 ... (remaining 226953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 817 or resid 1101 through 1102)) selection = chain 'B' selection = (chain 'C' and (resid 10 through 817 or resid 1101 through 1102)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.000 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 71.750 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.210 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:2.890 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 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 : 0.007 0.193 28162 Z= 0.474 Angle : 1.120 9.091 38088 Z= 0.782 Chirality : 0.042 0.156 4236 Planarity : 0.005 0.094 4768 Dihedral : 8.406 81.359 10326 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 1.77 % Allowed : 5.24 % Favored : 92.99 % Rotamer: Outliers : 0.17 % Allowed : 0.57 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % 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: -1.87 (0.13), residues: 3452 helix: -1.99 (0.08), residues: 1649 sheet: -2.56 (0.26), residues: 368 loop : 0.49 (0.18), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 198 HIS 0.006 0.001 HIS D 412 PHE 0.019 0.002 PHE A 574 TYR 0.019 0.002 TYR B 450 ARG 0.010 0.001 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 623 time to evaluate : 3.229 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: A 161 THR cc_start: 0.8435 (m) cc_final: 0.8217 (p) REVERT: A 365 THR cc_start: 0.9049 (m) cc_final: 0.8814 (p) REVERT: A 408 MET cc_start: 0.7709 (mmm) cc_final: 0.7423 (mmm) REVERT: A 440 TYR cc_start: 0.8721 (p90) cc_final: 0.8246 (p90) REVERT: A 442 LEU cc_start: 0.8635 (mt) cc_final: 0.8227 (mt) REVERT: A 496 MET cc_start: 0.7546 (ttm) cc_final: 0.7311 (mtp) REVERT: A 521 LEU cc_start: 0.9067 (tt) cc_final: 0.8549 (tp) REVERT: A 624 LEU cc_start: 0.9110 (mt) cc_final: 0.8460 (tp) REVERT: A 659 PHE cc_start: 0.9137 (m-80) cc_final: 0.8909 (m-80) REVERT: A 674 MET cc_start: 0.8838 (mtm) cc_final: 0.8559 (mtm) REVERT: A 734 ILE cc_start: 0.8617 (mm) cc_final: 0.8280 (mm) REVERT: B 193 ILE cc_start: 0.8837 (mt) cc_final: 0.8009 (mm) REVERT: B 221 ILE cc_start: 0.8582 (mt) cc_final: 0.8029 (mt) REVERT: B 245 PHE cc_start: 0.7833 (m-80) cc_final: 0.7492 (m-10) REVERT: B 403 SER cc_start: 0.8508 (m) cc_final: 0.8306 (p) REVERT: B 412 HIS cc_start: 0.8427 (p90) cc_final: 0.8003 (p90) REVERT: B 463 MET cc_start: 0.8124 (mtm) cc_final: 0.7785 (mtt) REVERT: B 521 LEU cc_start: 0.9352 (tt) cc_final: 0.8660 (tp) REVERT: B 526 TRP cc_start: 0.9099 (m100) cc_final: 0.8550 (m100) REVERT: B 670 MET cc_start: 0.8779 (mtp) cc_final: 0.8433 (mmt) REVERT: C 638 ASP cc_start: 0.9120 (m-30) cc_final: 0.8799 (m-30) REVERT: C 659 PHE cc_start: 0.9392 (m-80) cc_final: 0.8834 (m-80) REVERT: C 674 MET cc_start: 0.9076 (mtm) cc_final: 0.8563 (mtm) REVERT: C 734 ILE cc_start: 0.8650 (mm) cc_final: 0.8336 (mm) REVERT: D 89 CYS cc_start: 0.6879 (m) cc_final: 0.6601 (m) REVERT: D 193 ILE cc_start: 0.8797 (mt) cc_final: 0.8442 (mp) REVERT: D 201 VAL cc_start: 0.9275 (t) cc_final: 0.9016 (t) REVERT: D 221 ILE cc_start: 0.8700 (mt) cc_final: 0.8349 (mm) REVERT: D 245 PHE cc_start: 0.7675 (m-80) cc_final: 0.7439 (m-80) REVERT: D 361 MET cc_start: 0.6236 (mmm) cc_final: 0.5494 (tpp) REVERT: D 403 SER cc_start: 0.8569 (m) cc_final: 0.8332 (p) REVERT: D 463 MET cc_start: 0.7706 (mtm) cc_final: 0.7457 (mtt) REVERT: D 521 LEU cc_start: 0.9267 (tt) cc_final: 0.8722 (tp) REVERT: D 526 TRP cc_start: 0.9174 (m100) cc_final: 0.8674 (m100) REVERT: D 670 MET cc_start: 0.8792 (mtp) cc_final: 0.8221 (mmt) REVERT: E 146 CYS cc_start: 0.5438 (m) cc_final: 0.5122 (t) REVERT: F 146 CYS cc_start: 0.5462 (m) cc_final: 0.5157 (t) outliers start: 5 outliers final: 1 residues processed: 627 average time/residue: 0.4169 time to fit residues: 402.8682 Evaluate side-chains 314 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 0.5980 chunk 262 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 271 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 314 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 65 GLN A 129 GLN A 214 HIS A 246 GLN A 311 ASN A 337 GLN A 355 ASN A 392 GLN A 587 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 359 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN B 642 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 83 ASN C 147 GLN C 311 ASN C 325 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 587 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN D 714 GLN E 185 GLN E 228 ASN F 162 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 28162 Z= 0.175 Angle : 0.593 9.179 38088 Z= 0.311 Chirality : 0.041 0.220 4236 Planarity : 0.005 0.077 4768 Dihedral : 5.743 83.673 3934 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.91 % Favored : 95.45 % Rotamer: Outliers : 0.24 % Allowed : 1.28 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3452 helix: 0.51 (0.12), residues: 1630 sheet: -2.06 (0.26), residues: 372 loop : 0.08 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 766 HIS 0.005 0.001 HIS B 412 PHE 0.029 0.002 PHE E 21 TYR 0.025 0.002 TYR B 450 ARG 0.008 0.001 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 428 time to evaluate : 2.949 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: A 129 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8717 (pp30) REVERT: A 161 THR cc_start: 0.8651 (m) cc_final: 0.8289 (p) REVERT: A 408 MET cc_start: 0.7953 (mmm) cc_final: 0.7300 (mmm) REVERT: A 427 ASP cc_start: 0.9063 (m-30) cc_final: 0.8825 (m-30) REVERT: A 542 LEU cc_start: 0.8245 (mt) cc_final: 0.7800 (mt) REVERT: B 126 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8844 (mt-10) REVERT: B 521 LEU cc_start: 0.9322 (tt) cc_final: 0.8891 (tp) REVERT: B 526 TRP cc_start: 0.9119 (m100) cc_final: 0.8897 (m100) REVERT: C 14 ILE cc_start: 0.9252 (pt) cc_final: 0.8832 (pt) REVERT: C 85 ILE cc_start: 0.8944 (mm) cc_final: 0.8669 (tp) REVERT: C 232 LEU cc_start: 0.9191 (mp) cc_final: 0.8926 (pt) REVERT: C 361 MET cc_start: 0.8051 (mmm) cc_final: 0.7409 (tpp) REVERT: C 427 ASP cc_start: 0.8976 (m-30) cc_final: 0.8716 (m-30) REVERT: C 528 CYS cc_start: 0.9366 (m) cc_final: 0.8190 (m) REVERT: C 659 PHE cc_start: 0.9336 (m-80) cc_final: 0.8947 (m-80) REVERT: C 734 ILE cc_start: 0.8787 (mm) cc_final: 0.8571 (mm) REVERT: D 361 MET cc_start: 0.7199 (mmm) cc_final: 0.6665 (tpp) REVERT: D 428 LEU cc_start: 0.9348 (tt) cc_final: 0.8853 (mt) REVERT: D 521 LEU cc_start: 0.9300 (tt) cc_final: 0.8971 (tp) REVERT: D 526 TRP cc_start: 0.9200 (m100) cc_final: 0.8997 (m100) REVERT: D 612 ILE cc_start: 0.9343 (mm) cc_final: 0.9130 (mm) REVERT: D 670 MET cc_start: 0.8783 (mtp) cc_final: 0.8195 (mmm) REVERT: D 710 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8801 (tt0) REVERT: E 121 LYS cc_start: 0.8367 (mttt) cc_final: 0.8131 (tmtt) REVERT: E 181 MET cc_start: 0.7158 (mtp) cc_final: 0.6955 (mtm) REVERT: E 188 GLN cc_start: 0.7411 (tp-100) cc_final: 0.7148 (tp-100) REVERT: F 188 GLN cc_start: 0.7391 (tp-100) cc_final: 0.7147 (tp-100) outliers start: 7 outliers final: 0 residues processed: 432 average time/residue: 0.3829 time to fit residues: 264.9900 Evaluate side-chains 283 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 314 optimal weight: 3.9990 chunk 340 optimal weight: 1.9990 chunk 280 optimal weight: 0.3980 chunk 312 optimal weight: 4.9990 chunk 107 optimal weight: 0.0470 chunk 252 optimal weight: 5.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 392 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 65 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 214 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28162 Z= 0.144 Angle : 0.526 8.060 38088 Z= 0.275 Chirality : 0.039 0.187 4236 Planarity : 0.004 0.067 4768 Dihedral : 5.246 81.448 3934 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.14 % Favored : 95.28 % Rotamer: Outliers : 0.07 % Allowed : 1.69 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3452 helix: 1.27 (0.12), residues: 1670 sheet: -1.69 (0.26), residues: 372 loop : -0.04 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 526 HIS 0.006 0.001 HIS E 180 PHE 0.025 0.001 PHE A 531 TYR 0.017 0.001 TYR B 450 ARG 0.004 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 2.999 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: A 129 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8771 (pp30) REVERT: A 161 THR cc_start: 0.8758 (m) cc_final: 0.8133 (p) REVERT: A 194 LEU cc_start: 0.9417 (tp) cc_final: 0.9133 (tp) REVERT: A 291 VAL cc_start: 0.9415 (p) cc_final: 0.9210 (m) REVERT: A 408 MET cc_start: 0.7840 (mmm) cc_final: 0.7244 (mmm) REVERT: A 427 ASP cc_start: 0.9138 (m-30) cc_final: 0.8871 (m-30) REVERT: A 440 TYR cc_start: 0.8653 (p90) cc_final: 0.7904 (p90) REVERT: A 442 LEU cc_start: 0.8810 (mt) cc_final: 0.8232 (mt) REVERT: B 361 MET cc_start: 0.7168 (mmm) cc_final: 0.6449 (tpp) REVERT: B 517 PHE cc_start: 0.9056 (t80) cc_final: 0.8846 (t80) REVERT: B 521 LEU cc_start: 0.9298 (tt) cc_final: 0.8877 (tp) REVERT: B 526 TRP cc_start: 0.9141 (m100) cc_final: 0.8869 (m100) REVERT: B 710 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8861 (tt0) REVERT: C 14 ILE cc_start: 0.9279 (pt) cc_final: 0.8992 (mm) REVERT: C 427 ASP cc_start: 0.9036 (m-30) cc_final: 0.8796 (m-30) REVERT: C 659 PHE cc_start: 0.9310 (m-80) cc_final: 0.9051 (m-80) REVERT: C 674 MET cc_start: 0.9319 (mtm) cc_final: 0.9052 (ttm) REVERT: C 704 LEU cc_start: 0.7396 (tp) cc_final: 0.7111 (tp) REVERT: C 734 ILE cc_start: 0.8811 (mm) cc_final: 0.8534 (mm) REVERT: D 380 MET cc_start: 0.8498 (mtp) cc_final: 0.8024 (mtp) REVERT: D 521 LEU cc_start: 0.9275 (tt) cc_final: 0.8848 (tp) REVERT: D 526 TRP cc_start: 0.9235 (m100) cc_final: 0.8960 (m100) REVERT: D 605 TRP cc_start: 0.9043 (t-100) cc_final: 0.8496 (t60) REVERT: D 617 THR cc_start: 0.9182 (m) cc_final: 0.8948 (p) REVERT: D 670 MET cc_start: 0.8823 (mtp) cc_final: 0.8166 (mmm) REVERT: D 710 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8862 (tt0) REVERT: E 213 TRP cc_start: 0.6350 (m-10) cc_final: 0.6099 (m-10) outliers start: 2 outliers final: 0 residues processed: 359 average time/residue: 0.3871 time to fit residues: 223.6080 Evaluate side-chains 254 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 211 optimal weight: 0.0170 chunk 315 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 299 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 overall best weight: 3.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 311 ASN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 33 GLN F 15 ASN F 33 GLN F 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 28162 Z= 0.312 Angle : 0.674 11.176 38088 Z= 0.359 Chirality : 0.043 0.209 4236 Planarity : 0.005 0.077 4768 Dihedral : 5.714 79.460 3934 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.14 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3452 helix: 1.15 (0.13), residues: 1657 sheet: -1.68 (0.25), residues: 367 loop : -0.19 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 130 HIS 0.011 0.002 HIS D 412 PHE 0.030 0.002 PHE A 584 TYR 0.019 0.002 TYR B 356 ARG 0.031 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 3.279 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: A 408 MET cc_start: 0.8576 (mmm) cc_final: 0.8155 (mmm) REVERT: A 427 ASP cc_start: 0.9423 (m-30) cc_final: 0.9175 (m-30) REVERT: A 526 TRP cc_start: 0.9157 (m100) cc_final: 0.8863 (m100) REVERT: A 542 LEU cc_start: 0.8263 (mt) cc_final: 0.8011 (mt) REVERT: A 626 VAL cc_start: 0.9405 (t) cc_final: 0.8930 (t) REVERT: A 629 MET cc_start: 0.7905 (ptp) cc_final: 0.7644 (ptt) REVERT: A 674 MET cc_start: 0.9147 (ttm) cc_final: 0.8541 (mmm) REVERT: B 33 MET cc_start: 0.8630 (ptt) cc_final: 0.8185 (ptt) REVERT: B 408 MET cc_start: 0.8256 (mmm) cc_final: 0.7766 (mmm) REVERT: C 113 MET cc_start: 0.9552 (mmp) cc_final: 0.9278 (mmp) REVERT: C 201 VAL cc_start: 0.9647 (t) cc_final: 0.9327 (t) REVERT: C 399 THR cc_start: 0.8479 (m) cc_final: 0.8143 (m) REVERT: C 407 MET cc_start: 0.7612 (mpp) cc_final: 0.7337 (mpp) REVERT: C 408 MET cc_start: 0.8875 (mmp) cc_final: 0.8350 (mmm) REVERT: C 427 ASP cc_start: 0.9343 (m-30) cc_final: 0.9052 (m-30) REVERT: C 463 MET cc_start: 0.8992 (mmt) cc_final: 0.8582 (mmt) REVERT: C 659 PHE cc_start: 0.9303 (m-80) cc_final: 0.9102 (m-80) REVERT: D 235 ILE cc_start: 0.9826 (pt) cc_final: 0.9441 (tp) REVERT: D 360 ILE cc_start: 0.9199 (pt) cc_final: 0.8979 (mp) REVERT: D 380 MET cc_start: 0.8818 (mtp) cc_final: 0.8359 (mtp) REVERT: D 463 MET cc_start: 0.8803 (ptp) cc_final: 0.8305 (pmm) REVERT: D 605 TRP cc_start: 0.9242 (t-100) cc_final: 0.8844 (t60) REVERT: D 609 THR cc_start: 0.9543 (t) cc_final: 0.9283 (p) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.3822 time to fit residues: 166.6990 Evaluate side-chains 192 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN E 228 ASN F 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28162 Z= 0.277 Angle : 0.615 8.751 38088 Z= 0.326 Chirality : 0.041 0.196 4236 Planarity : 0.005 0.073 4768 Dihedral : 5.489 66.951 3934 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.43 % Favored : 95.08 % Rotamer: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3452 helix: 1.35 (0.13), residues: 1624 sheet: -1.40 (0.26), residues: 384 loop : -0.31 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 213 HIS 0.011 0.002 HIS B 412 PHE 0.060 0.002 PHE A 584 TYR 0.022 0.002 TYR D 421 ARG 0.007 0.001 ARG D 675 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 3.285 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: A 408 MET cc_start: 0.8626 (mmm) cc_final: 0.8379 (mmm) REVERT: A 674 MET cc_start: 0.8964 (ttm) cc_final: 0.8483 (mmm) REVERT: B 33 MET cc_start: 0.8926 (ptt) cc_final: 0.8451 (ptt) REVERT: B 361 MET cc_start: 0.8509 (mmm) cc_final: 0.8022 (tpp) REVERT: B 408 MET cc_start: 0.8098 (mmm) cc_final: 0.7627 (mmm) REVERT: B 412 HIS cc_start: 0.8252 (p90) cc_final: 0.7772 (p90) REVERT: B 585 MET cc_start: 0.4812 (ptp) cc_final: 0.2966 (ptt) REVERT: C 113 MET cc_start: 0.9465 (mmp) cc_final: 0.9179 (mmp) REVERT: C 608 PHE cc_start: 0.9261 (t80) cc_final: 0.8936 (t80) REVERT: C 674 MET cc_start: 0.9469 (mtm) cc_final: 0.8514 (mmm) REVERT: D 33 MET cc_start: 0.8955 (ptt) cc_final: 0.8446 (ptt) REVERT: D 235 ILE cc_start: 0.9868 (pt) cc_final: 0.9639 (tp) REVERT: D 361 MET cc_start: 0.8740 (mmm) cc_final: 0.8197 (mmm) REVERT: D 605 TRP cc_start: 0.9081 (t-100) cc_final: 0.8717 (t60) REVERT: E 121 LYS cc_start: 0.6074 (tmtt) cc_final: 0.5722 (tmtt) REVERT: F 121 LYS cc_start: 0.5545 (tmtt) cc_final: 0.5109 (tmtt) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.3626 time to fit residues: 145.2196 Evaluate side-chains 175 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 0.5980 chunk 301 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 196 optimal weight: 0.2980 chunk 82 optimal weight: 9.9990 chunk 334 optimal weight: 0.0370 chunk 277 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 65 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 355 ASN B 412 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28162 Z= 0.138 Angle : 0.525 7.938 38088 Z= 0.271 Chirality : 0.039 0.196 4236 Planarity : 0.004 0.072 4768 Dihedral : 4.940 60.536 3934 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.77 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3452 helix: 1.64 (0.13), residues: 1661 sheet: -1.24 (0.26), residues: 388 loop : -0.35 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 262 HIS 0.005 0.001 HIS E 180 PHE 0.018 0.001 PHE A 584 TYR 0.015 0.001 TYR C 616 ARG 0.012 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 3.070 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: A 194 LEU cc_start: 0.8961 (tp) cc_final: 0.8560 (tp) REVERT: A 408 MET cc_start: 0.8555 (mmm) cc_final: 0.7744 (mmm) REVERT: A 674 MET cc_start: 0.8989 (ttm) cc_final: 0.8571 (mmm) REVERT: A 721 MET cc_start: 0.8594 (pmm) cc_final: 0.8111 (pmm) REVERT: B 33 MET cc_start: 0.8750 (ptt) cc_final: 0.8350 (ptt) REVERT: B 361 MET cc_start: 0.8494 (mmm) cc_final: 0.7952 (tpp) REVERT: B 408 MET cc_start: 0.7952 (mmm) cc_final: 0.7582 (mmm) REVERT: B 412 HIS cc_start: 0.8404 (p-80) cc_final: 0.7897 (p-80) REVERT: C 194 LEU cc_start: 0.8837 (tp) cc_final: 0.8471 (tp) REVERT: C 424 TYR cc_start: 0.9324 (t80) cc_final: 0.8810 (t80) REVERT: C 463 MET cc_start: 0.9143 (mmt) cc_final: 0.8592 (mmt) REVERT: C 496 MET cc_start: 0.8952 (mmp) cc_final: 0.8731 (mmm) REVERT: C 608 PHE cc_start: 0.9097 (t80) cc_final: 0.8633 (t80) REVERT: C 674 MET cc_start: 0.9531 (mtm) cc_final: 0.8640 (mmm) REVERT: C 704 LEU cc_start: 0.8624 (tp) cc_final: 0.8404 (tt) REVERT: D 33 MET cc_start: 0.8962 (ptt) cc_final: 0.8518 (ptt) REVERT: D 235 ILE cc_start: 0.9867 (pt) cc_final: 0.9563 (mm) REVERT: D 284 LEU cc_start: 0.9602 (mm) cc_final: 0.9269 (mt) REVERT: D 361 MET cc_start: 0.8879 (mmm) cc_final: 0.8373 (tpp) REVERT: D 463 MET cc_start: 0.8799 (pmm) cc_final: 0.8588 (pmm) REVERT: D 496 MET cc_start: 0.8719 (ppp) cc_final: 0.8516 (ppp) REVERT: D 605 TRP cc_start: 0.9064 (t-100) cc_final: 0.8751 (t60) REVERT: F 121 LYS cc_start: 0.5450 (tmtt) cc_final: 0.5035 (tmtt) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3763 time to fit residues: 154.6726 Evaluate side-chains 184 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 333 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.8368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28162 Z= 0.252 Angle : 0.579 9.233 38088 Z= 0.305 Chirality : 0.040 0.190 4236 Planarity : 0.004 0.073 4768 Dihedral : 5.101 56.252 3934 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.72 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3452 helix: 1.59 (0.13), residues: 1656 sheet: -1.18 (0.26), residues: 398 loop : -0.33 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 213 HIS 0.012 0.002 HIS A 219 PHE 0.029 0.002 PHE A 584 TYR 0.022 0.001 TYR F 205 ARG 0.011 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.217 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: A 380 MET cc_start: 0.8476 (ppp) cc_final: 0.8224 (ppp) REVERT: A 674 MET cc_start: 0.9067 (ttm) cc_final: 0.8623 (mmm) REVERT: A 721 MET cc_start: 0.8252 (pmm) cc_final: 0.7870 (pmm) REVERT: B 33 MET cc_start: 0.8886 (ptt) cc_final: 0.8371 (ptt) REVERT: B 361 MET cc_start: 0.8676 (mmm) cc_final: 0.8013 (tpp) REVERT: B 408 MET cc_start: 0.8271 (mmm) cc_final: 0.7815 (mmm) REVERT: B 412 HIS cc_start: 0.8376 (p-80) cc_final: 0.7999 (p-80) REVERT: C 113 MET cc_start: 0.9396 (mmp) cc_final: 0.9164 (mmp) REVERT: C 463 MET cc_start: 0.9039 (mmt) cc_final: 0.8651 (mmt) REVERT: C 496 MET cc_start: 0.9321 (mmp) cc_final: 0.9076 (mmm) REVERT: C 608 PHE cc_start: 0.9219 (t80) cc_final: 0.8832 (t80) REVERT: C 674 MET cc_start: 0.9543 (mtm) cc_final: 0.8657 (mmm) REVERT: D 33 MET cc_start: 0.9020 (ptt) cc_final: 0.8517 (ptt) REVERT: D 235 ILE cc_start: 0.9874 (pt) cc_final: 0.9668 (tp) REVERT: D 463 MET cc_start: 0.8742 (pmm) cc_final: 0.8533 (pmm) REVERT: D 496 MET cc_start: 0.8729 (ppp) cc_final: 0.8363 (ppp) REVERT: D 585 MET cc_start: 0.4392 (ptt) cc_final: 0.2135 (ptt) REVERT: D 604 VAL cc_start: 0.9325 (m) cc_final: 0.9109 (p) REVERT: D 708 MET cc_start: 0.8978 (mmm) cc_final: 0.8606 (tpp) REVERT: E 121 LYS cc_start: 0.5528 (tmtt) cc_final: 0.5293 (tmtt) REVERT: F 121 LYS cc_start: 0.5346 (tmtt) cc_final: 0.4770 (tmtt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3683 time to fit residues: 136.4205 Evaluate side-chains 172 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 199 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 262 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.8657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28162 Z= 0.176 Angle : 0.537 9.917 38088 Z= 0.278 Chirality : 0.039 0.201 4236 Planarity : 0.004 0.073 4768 Dihedral : 4.877 57.954 3934 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.29 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3452 helix: 1.70 (0.13), residues: 1661 sheet: -1.05 (0.26), residues: 400 loop : -0.40 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 31 HIS 0.005 0.001 HIS A 219 PHE 0.025 0.001 PHE F 21 TYR 0.013 0.001 TYR B 732 ARG 0.005 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 3.193 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: A 380 MET cc_start: 0.8426 (ppp) cc_final: 0.8163 (ppp) REVERT: A 629 MET cc_start: 0.8061 (ptp) cc_final: 0.7835 (ptp) REVERT: A 674 MET cc_start: 0.9032 (ttm) cc_final: 0.8679 (mmm) REVERT: B 33 MET cc_start: 0.8807 (ptt) cc_final: 0.8313 (ptt) REVERT: B 361 MET cc_start: 0.8745 (mmm) cc_final: 0.8058 (tpp) REVERT: B 408 MET cc_start: 0.8194 (mmm) cc_final: 0.7901 (mmm) REVERT: C 113 MET cc_start: 0.9325 (mmp) cc_final: 0.9092 (mmp) REVERT: C 496 MET cc_start: 0.9267 (mmp) cc_final: 0.9067 (mmm) REVERT: C 608 PHE cc_start: 0.9108 (t80) cc_final: 0.8702 (t80) REVERT: C 674 MET cc_start: 0.9548 (mtm) cc_final: 0.8692 (mmm) REVERT: C 704 LEU cc_start: 0.8738 (tp) cc_final: 0.8524 (tt) REVERT: D 33 MET cc_start: 0.8981 (ptt) cc_final: 0.8459 (ptt) REVERT: D 235 ILE cc_start: 0.9864 (pt) cc_final: 0.9588 (mm) REVERT: D 361 MET cc_start: 0.8914 (mmt) cc_final: 0.8505 (tpp) REVERT: D 463 MET cc_start: 0.8732 (pmm) cc_final: 0.8504 (pmm) REVERT: D 496 MET cc_start: 0.8769 (ppp) cc_final: 0.8568 (ppp) REVERT: D 670 MET cc_start: 0.9249 (ppp) cc_final: 0.9018 (ppp) REVERT: E 121 LYS cc_start: 0.5665 (tmtt) cc_final: 0.5369 (tmtt) REVERT: F 121 LYS cc_start: 0.5603 (tmtt) cc_final: 0.4962 (tmtt) REVERT: F 188 GLN cc_start: 0.7347 (tp-100) cc_final: 0.7083 (tp-100) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3665 time to fit residues: 135.0789 Evaluate side-chains 173 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 291 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 280 optimal weight: 0.1980 chunk 293 optimal weight: 5.9990 chunk 309 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN F 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.8825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28162 Z= 0.142 Angle : 0.524 9.953 38088 Z= 0.269 Chirality : 0.039 0.189 4236 Planarity : 0.004 0.071 4768 Dihedral : 4.650 58.708 3934 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.20 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3452 helix: 1.74 (0.13), residues: 1673 sheet: -0.89 (0.26), residues: 398 loop : -0.44 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 213 HIS 0.004 0.001 HIS A 219 PHE 0.020 0.001 PHE B 623 TYR 0.011 0.001 TYR C 77 ARG 0.003 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.644 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: A 380 MET cc_start: 0.8418 (ppp) cc_final: 0.8168 (ppp) REVERT: A 442 LEU cc_start: 0.9194 (mt) cc_final: 0.8982 (mt) REVERT: A 528 CYS cc_start: 0.9370 (m) cc_final: 0.9047 (t) REVERT: A 629 MET cc_start: 0.8009 (ptp) cc_final: 0.7793 (ptp) REVERT: A 674 MET cc_start: 0.8977 (ttm) cc_final: 0.8669 (mmm) REVERT: A 721 MET cc_start: 0.8405 (pmm) cc_final: 0.7932 (pmm) REVERT: B 33 MET cc_start: 0.8794 (ptt) cc_final: 0.8302 (ptt) REVERT: B 235 ILE cc_start: 0.9865 (pt) cc_final: 0.9554 (mm) REVERT: B 361 MET cc_start: 0.8707 (mmm) cc_final: 0.7999 (tpp) REVERT: B 408 MET cc_start: 0.8150 (mmm) cc_final: 0.7636 (mmm) REVERT: B 412 HIS cc_start: 0.8503 (p-80) cc_final: 0.8009 (p-80) REVERT: B 496 MET cc_start: 0.8913 (ppp) cc_final: 0.8165 (ppp) REVERT: B 807 MET cc_start: 0.8577 (mmp) cc_final: 0.8353 (mmp) REVERT: C 113 MET cc_start: 0.9322 (mmp) cc_final: 0.9059 (mmp) REVERT: C 424 TYR cc_start: 0.9407 (t80) cc_final: 0.8936 (t80) REVERT: C 608 PHE cc_start: 0.9028 (t80) cc_final: 0.8600 (t80) REVERT: C 674 MET cc_start: 0.9557 (mtm) cc_final: 0.8750 (mmm) REVERT: C 704 LEU cc_start: 0.8658 (tp) cc_final: 0.8432 (tt) REVERT: D 33 MET cc_start: 0.8963 (ptt) cc_final: 0.8424 (ptt) REVERT: D 235 ILE cc_start: 0.9857 (pt) cc_final: 0.9596 (mm) REVERT: D 361 MET cc_start: 0.8901 (mmt) cc_final: 0.8605 (tpp) REVERT: D 463 MET cc_start: 0.8798 (pmm) cc_final: 0.8568 (pmm) REVERT: D 670 MET cc_start: 0.9210 (ppp) cc_final: 0.8973 (ppp) REVERT: E 121 LYS cc_start: 0.5350 (tmtt) cc_final: 0.5088 (tmtt) REVERT: F 121 LYS cc_start: 0.5396 (tmtt) cc_final: 0.4755 (tmtt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3696 time to fit residues: 137.9568 Evaluate side-chains 178 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 0.9990 chunk 328 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 344 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 274 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN B 65 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN F 162 ASN F 185 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.9010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28162 Z= 0.153 Angle : 0.531 9.648 38088 Z= 0.272 Chirality : 0.039 0.223 4236 Planarity : 0.004 0.070 4768 Dihedral : 4.551 59.419 3934 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.20 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3452 helix: 1.79 (0.13), residues: 1652 sheet: -0.87 (0.26), residues: 396 loop : -0.45 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 213 HIS 0.004 0.001 HIS A 219 PHE 0.029 0.001 PHE F 21 TYR 0.013 0.001 TYR A 135 ARG 0.004 0.000 ARG C 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 3.287 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: A 380 MET cc_start: 0.8445 (ppp) cc_final: 0.8208 (ppp) REVERT: A 629 MET cc_start: 0.8005 (ptp) cc_final: 0.7775 (ptp) REVERT: A 674 MET cc_start: 0.8986 (ttm) cc_final: 0.8678 (mmm) REVERT: A 721 MET cc_start: 0.8388 (pmm) cc_final: 0.7939 (pmm) REVERT: B 33 MET cc_start: 0.8802 (ptt) cc_final: 0.8305 (ptt) REVERT: B 361 MET cc_start: 0.8735 (mmm) cc_final: 0.7994 (tpp) REVERT: B 408 MET cc_start: 0.8216 (mmm) cc_final: 0.7876 (mmm) REVERT: B 496 MET cc_start: 0.8980 (ppp) cc_final: 0.8717 (ppp) REVERT: C 113 MET cc_start: 0.9332 (mmp) cc_final: 0.9088 (mmp) REVERT: C 424 TYR cc_start: 0.9416 (t80) cc_final: 0.8902 (t80) REVERT: C 608 PHE cc_start: 0.9025 (t80) cc_final: 0.8668 (t80) REVERT: C 674 MET cc_start: 0.9558 (mtm) cc_final: 0.8846 (mmm) REVERT: C 704 LEU cc_start: 0.8660 (tp) cc_final: 0.8432 (tt) REVERT: D 33 MET cc_start: 0.8965 (ptt) cc_final: 0.8404 (ptt) REVERT: D 235 ILE cc_start: 0.9861 (pt) cc_final: 0.9597 (mm) REVERT: D 361 MET cc_start: 0.8930 (mmt) cc_final: 0.8644 (tpp) REVERT: D 463 MET cc_start: 0.8812 (pmm) cc_final: 0.8592 (pmm) REVERT: D 496 MET cc_start: 0.8863 (ppp) cc_final: 0.8615 (ppp) REVERT: D 604 VAL cc_start: 0.9233 (m) cc_final: 0.8944 (p) REVERT: D 670 MET cc_start: 0.9198 (ppp) cc_final: 0.8971 (ppp) REVERT: E 121 LYS cc_start: 0.5380 (tmtt) cc_final: 0.4824 (tmtt) REVERT: F 121 LYS cc_start: 0.5462 (tmtt) cc_final: 0.4924 (tmtt) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3674 time to fit residues: 135.9990 Evaluate side-chains 175 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 274 optimal weight: 0.0980 chunk 115 optimal weight: 9.9990 chunk 282 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN F 162 ASN F 185 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.044648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.033542 restraints weight = 209782.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.034700 restraints weight = 131102.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.035473 restraints weight = 93964.507| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.9296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28162 Z= 0.168 Angle : 0.530 9.518 38088 Z= 0.274 Chirality : 0.039 0.173 4236 Planarity : 0.004 0.073 4768 Dihedral : 4.549 58.919 3934 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.40 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3452 helix: 1.80 (0.13), residues: 1656 sheet: -0.94 (0.27), residues: 368 loop : -0.45 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 526 HIS 0.004 0.001 HIS A 219 PHE 0.025 0.001 PHE B 74 TYR 0.012 0.001 TYR A 77 ARG 0.008 0.000 ARG C 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4914.87 seconds wall clock time: 91 minutes 47.45 seconds (5507.45 seconds total)