Starting phenix.real_space_refine on Mon Feb 19 01:27:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm6_13522/02_2024/7pm6_13522_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm6_13522/02_2024/7pm6_13522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm6_13522/02_2024/7pm6_13522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm6_13522/02_2024/7pm6_13522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm6_13522/02_2024/7pm6_13522_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm6_13522/02_2024/7pm6_13522_updated.pdb" } resolution = 3.0 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= 0.001 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 10 5.49 5 Mg 5 5.21 5 S 148 5.16 5 C 14835 2.51 5 N 3957 2.21 5 O 4379 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 511": "OE1" <-> "OE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 768": "NH1" <-> "NH2" Residue "D TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 789": "NH1" <-> "NH2" Residue "D ARG 791": "NH1" <-> "NH2" Residue "D ARG 792": "NH1" <-> "NH2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23334 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.04, per 1000 atoms: 0.52 Number of scatterers: 23334 At special positions: 0 Unit cell: (171.72, 224.72, 177.02, 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 148 16.00 P 10 15.00 Mg 5 11.99 O 4379 8.00 N 3957 7.00 C 14835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 10.14 Conformation dependent library (CDL) restraints added in 4.4 seconds 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 5456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 30 sheets defined 47.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.213A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.561A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.567A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.576A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.526A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 301 through 314 removed outlier: 3.959A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.869A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.909A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 480 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.598A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.586A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 704 through 714 removed outlier: 6.611A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.881A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.501A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.542A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.229A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.749A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.680A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.592A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.939A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.125A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 78 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 96 removed outlier: 4.657A pdb=" N PHE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 139 through 152 removed outlier: 3.584A pdb=" N ALA D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 183 removed outlier: 3.653A pdb=" N PHE D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 207 removed outlier: 3.576A pdb=" N ASN D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 246 through 249 Processing helix chain 'D' and resid 260 through 268 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 301 through 315 removed outlier: 3.870A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 337 removed outlier: 3.916A pdb=" N ASN D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 368 through 376 removed outlier: 3.814A pdb=" N CYS D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 423 Processing helix chain 'D' and resid 449 through 479 Processing helix chain 'D' and resid 484 through 486 No H-bonds generated for 'chain 'D' and resid 484 through 486' Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.775A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 587 through 593 removed outlier: 3.561A pdb=" N GLU D 591 " --> pdb=" O LYS D 587 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 633 No H-bonds generated for 'chain 'D' and resid 630 through 633' Processing helix chain 'D' and resid 636 through 652 Processing helix chain 'D' and resid 675 through 684 removed outlier: 3.615A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 704 through 714 removed outlier: 6.612A pdb=" N VAL D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 735 removed outlier: 3.987A pdb=" N GLU D 733 " --> pdb=" O LYS D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 741 No H-bonds generated for 'chain 'D' and resid 739 through 741' Processing helix chain 'D' and resid 755 through 791 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 removed outlier: 3.705A pdb=" N MET F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.519A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 4.232A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.798A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 261 removed outlier: 4.203A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.657A pdb=" N LYS F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 318 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.012A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 removed outlier: 3.912A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 372 Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 removed outlier: 3.616A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.529A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 4.147A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 removed outlier: 3.726A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 252 through 261 removed outlier: 4.274A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 284 removed outlier: 3.629A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 294 removed outlier: 3.634A pdb=" N ARG G 290 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS G 291 " --> pdb=" O ASP G 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR G 294 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 318 Processing helix chain 'G' and resid 338 through 348 removed outlier: 3.588A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 3.983A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 372 Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.544A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.564A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= F, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= G, first strand: chain 'A' and resid 700 through 703 Processing sheet with id= H, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.321A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.541A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= N, first strand: chain 'E' and resid 26 through 28 Processing sheet with id= O, first strand: chain 'D' and resid 12 through 16 Processing sheet with id= P, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.792A pdb=" N GLY D 163 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 377 through 381 Processing sheet with id= R, first strand: chain 'D' and resid 547 through 551 Processing sheet with id= S, first strand: chain 'D' and resid 700 through 703 Processing sheet with id= T, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.226A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= V, first strand: chain 'F' and resid 34 through 38 Processing sheet with id= W, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= X, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.487A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Z, first strand: chain 'G' and resid 8 through 12 Processing sheet with id= AA, first strand: chain 'G' and resid 34 through 38 Processing sheet with id= AB, first strand: chain 'G' and resid 103 through 107 Processing sheet with id= AC, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.489A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 972 hydrogen bonds defined for protein. 2712 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: 8.43 Time building geometry restraints manager: 10.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3893 1.31 - 1.44: 6320 1.44 - 1.56: 13364 1.56 - 1.69: 15 1.69 - 1.82: 242 Bond restraints: 23834 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.432 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.435 0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.469 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" CA TRP J 1 " pdb=" C TRP J 1 " ideal model delta sigma weight residual 1.525 1.441 0.084 2.10e-02 2.27e+03 1.60e+01 bond pdb=" C EEP I 2 " pdb=" O EEP I 2 " ideal model delta sigma weight residual 1.263 1.189 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 23829 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.57: 457 104.57 - 112.57: 12131 112.57 - 120.57: 11519 120.57 - 128.57: 7927 128.57 - 136.57: 189 Bond angle restraints: 32223 Sorted by residual: angle pdb=" N TYR D 113 " pdb=" CA TYR D 113 " pdb=" CB TYR D 113 " ideal model delta sigma weight residual 113.15 103.69 9.46 1.63e+00 3.76e-01 3.37e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 111.40 10.30 1.80e+00 3.09e-01 3.27e+01 angle pdb=" N CYS I 5 " pdb=" CA CYS I 5 " pdb=" CB CYS I 5 " ideal model delta sigma weight residual 110.50 100.85 9.65 1.70e+00 3.46e-01 3.23e+01 angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 111.59 10.11 1.80e+00 3.09e-01 3.15e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 112.42 9.28 1.80e+00 3.09e-01 2.66e+01 ... (remaining 32218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.86: 13864 27.86 - 55.73: 408 55.73 - 83.59: 68 83.59 - 111.46: 12 111.46 - 139.32: 12 Dihedral angle restraints: 14364 sinusoidal: 5893 harmonic: 8471 Sorted by residual: dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.32 -139.32 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.28 -139.28 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.04 -139.04 1 2.00e+01 2.50e-03 4.21e+01 ... (remaining 14361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2230 0.055 - 0.110: 1012 0.110 - 0.165: 237 0.165 - 0.219: 35 0.219 - 0.274: 12 Chirality restraints: 3526 Sorted by residual: chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False -2.53 -2.25 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU A 782 " pdb=" CB LEU A 782 " pdb=" CD1 LEU A 782 " pdb=" CD2 LEU A 782 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA CYS I 5 " pdb=" N CYS I 5 " pdb=" C CYS I 5 " pdb=" CB CYS I 5 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3523 not shown) Planarity restraints: 4112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 113 " 0.057 2.00e-02 2.50e+03 4.60e-02 4.22e+01 pdb=" CG TYR D 113 " -0.106 2.00e-02 2.50e+03 pdb=" CD1 TYR D 113 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 113 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 113 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR D 113 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR D 113 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR D 113 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.077 9.50e-02 1.11e+02 4.67e-02 1.30e+01 pdb=" NE ARG A 677 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 677 " 0.079 9.50e-02 1.11e+02 4.69e-02 1.26e+01 pdb=" NE ARG D 677 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 677 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG D 677 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG D 677 " -0.017 2.00e-02 2.50e+03 ... (remaining 4109 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 8 2.02 - 2.74: 3044 2.74 - 3.46: 32844 3.46 - 4.18: 55993 4.18 - 4.90: 100721 Nonbonded interactions: 192610 Sorted by model distance: nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.304 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.309 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.311 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.724 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.727 3.620 ... (remaining 192605 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 2.100 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: 8.200 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 65.930 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.190 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.012 0.140 23834 Z= 0.793 Angle : 1.073 14.493 32223 Z= 0.594 Chirality : 0.063 0.274 3526 Planarity : 0.007 0.047 4112 Dihedral : 14.942 139.320 8908 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.44 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 2839 helix: -1.51 (0.12), residues: 1335 sheet: 0.01 (0.24), residues: 404 loop : 0.28 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP C 356 HIS 0.014 0.003 HIS A 260 PHE 0.042 0.004 PHE D 564 TYR 0.106 0.006 TYR D 113 ARG 0.061 0.009 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 2.685 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: C 355 MET cc_start: 0.8143 (mmm) cc_final: 0.7891 (mmt) REVERT: C 360 GLN cc_start: 0.8220 (tp40) cc_final: 0.7382 (tm-30) REVERT: E 120 MET cc_start: 0.4648 (mtm) cc_final: 0.4233 (mtt) REVERT: F 82 MET cc_start: 0.8444 (tpt) cc_final: 0.8142 (tpt) REVERT: G 360 GLN cc_start: 0.8238 (tp40) cc_final: 0.8011 (tp-100) outliers start: 1 outliers final: 3 residues processed: 267 average time/residue: 1.8457 time to fit residues: 546.4917 Evaluate side-chains 136 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 119 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 86 optimal weight: 40.0000 chunk 135 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 214 ASN A 264 GLN A 463 GLN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 280 ASN E 75 GLN D 264 GLN D 395 HIS D 410 ASN D 418 HIS ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 280 ASN G 280 ASN G 297 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23834 Z= 0.204 Angle : 0.659 10.971 32223 Z= 0.335 Chirality : 0.044 0.250 3526 Planarity : 0.004 0.037 4112 Dihedral : 10.348 136.747 3257 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.69 % Allowed : 6.12 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 2839 helix: 0.38 (0.14), residues: 1332 sheet: 0.53 (0.24), residues: 418 loop : 0.82 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 1 HIS 0.006 0.001 HIS F 275 PHE 0.026 0.002 PHE C 255 TYR 0.045 0.001 TYR D 113 ARG 0.010 0.001 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 2.977 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: A 305 MET cc_start: 0.7238 (tmm) cc_final: 0.7036 (ppp) REVERT: C 176 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7451 (mpt) REVERT: E 120 MET cc_start: 0.5330 (mtm) cc_final: 0.4627 (mtp) outliers start: 42 outliers final: 9 residues processed: 180 average time/residue: 1.5634 time to fit residues: 318.9064 Evaluate side-chains 136 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 292 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 259 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 GLN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23834 Z= 0.349 Angle : 0.648 11.011 32223 Z= 0.326 Chirality : 0.045 0.303 3526 Planarity : 0.004 0.043 4112 Dihedral : 9.375 140.039 3252 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.26 % Allowed : 7.49 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2839 helix: 0.77 (0.14), residues: 1351 sheet: 0.67 (0.25), residues: 402 loop : 0.70 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 484 HIS 0.005 0.001 HIS D 418 PHE 0.016 0.002 PHE C 255 TYR 0.032 0.002 TYR D 113 ARG 0.007 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 2.880 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: B 120 MET cc_start: 0.3691 (mtm) cc_final: 0.3033 (mmm) REVERT: C 176 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7476 (mpt) REVERT: E 120 MET cc_start: 0.5251 (mtm) cc_final: 0.1539 (mmt) REVERT: F 12 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: G 314 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8193 (tt0) outliers start: 56 outliers final: 14 residues processed: 172 average time/residue: 1.4849 time to fit residues: 291.1911 Evaluate side-chains 139 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 134 optimal weight: 0.0970 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 275 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 246 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23834 Z= 0.159 Angle : 0.572 10.001 32223 Z= 0.282 Chirality : 0.041 0.233 3526 Planarity : 0.003 0.052 4112 Dihedral : 8.851 139.385 3252 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.89 % Allowed : 8.86 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2839 helix: 1.15 (0.15), residues: 1334 sheet: 0.69 (0.26), residues: 398 loop : 0.74 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 781 HIS 0.005 0.001 HIS F 275 PHE 0.016 0.001 PHE G 255 TYR 0.020 0.001 TYR A 787 ARG 0.004 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 2.828 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: B 120 MET cc_start: 0.3663 (mtm) cc_final: 0.2813 (mmm) REVERT: C 176 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7468 (mpt) REVERT: E 105 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7322 (ptp) REVERT: E 120 MET cc_start: 0.5615 (mtm) cc_final: 0.5034 (mtp) REVERT: D 715 MET cc_start: 0.1256 (mpt) cc_final: 0.0811 (mmt) REVERT: D 749 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8597 (tp) REVERT: F 12 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7540 (m-40) REVERT: G 176 MET cc_start: 0.7855 (mtt) cc_final: 0.7602 (mtt) outliers start: 47 outliers final: 13 residues processed: 173 average time/residue: 1.5586 time to fit residues: 305.8883 Evaluate side-chains 140 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 205 optimal weight: 20.0000 chunk 113 optimal weight: 0.3980 chunk 235 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 140 optimal weight: 0.2980 chunk 247 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 HIS ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23834 Z= 0.152 Angle : 0.563 8.817 32223 Z= 0.275 Chirality : 0.041 0.300 3526 Planarity : 0.003 0.047 4112 Dihedral : 8.471 140.227 3252 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.93 % Allowed : 9.75 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.16), residues: 2839 helix: 1.25 (0.15), residues: 1339 sheet: 0.62 (0.25), residues: 422 loop : 0.71 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 781 HIS 0.005 0.001 HIS D 418 PHE 0.033 0.001 PHE D 360 TYR 0.019 0.001 TYR A 787 ARG 0.008 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 135 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.3025 (m-80) cc_final: 0.2810 (m-80) REVERT: B 120 MET cc_start: 0.3735 (mtm) cc_final: 0.2969 (mmm) REVERT: A 749 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8567 (tp) REVERT: C 176 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7416 (mpt) REVERT: C 276 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: E 105 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7344 (ptp) REVERT: E 120 MET cc_start: 0.5203 (mtm) cc_final: 0.1757 (mmt) REVERT: D 203 MET cc_start: 0.7858 (mmm) cc_final: 0.7582 (mtt) REVERT: D 715 MET cc_start: 0.1352 (mpt) cc_final: 0.1033 (mmt) REVERT: F 72 GLU cc_start: 0.7344 (pm20) cc_final: 0.7065 (pm20) REVERT: G 176 MET cc_start: 0.7874 (mtt) cc_final: 0.7649 (mtt) outliers start: 48 outliers final: 13 residues processed: 166 average time/residue: 1.5139 time to fit residues: 286.5464 Evaluate side-chains 143 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 91 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23834 Z= 0.309 Angle : 0.603 7.908 32223 Z= 0.297 Chirality : 0.043 0.200 3526 Planarity : 0.004 0.046 4112 Dihedral : 8.409 143.116 3252 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.77 % Allowed : 10.76 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2839 helix: 1.25 (0.15), residues: 1354 sheet: 0.56 (0.25), residues: 418 loop : 0.63 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 702 HIS 0.007 0.001 HIS A 418 PHE 0.023 0.001 PHE D 360 TYR 0.020 0.001 TYR A 787 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4066 (mtm) cc_final: 0.3247 (mmm) REVERT: C 176 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7468 (mpt) REVERT: C 314 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: E 105 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7445 (ptp) REVERT: E 120 MET cc_start: 0.5189 (mtm) cc_final: 0.1756 (mmt) REVERT: D 715 MET cc_start: 0.1403 (mpt) cc_final: 0.0974 (mmt) REVERT: G 176 MET cc_start: 0.7910 (mtt) cc_final: 0.7709 (mtt) REVERT: G 355 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7558 (mmm) outliers start: 44 outliers final: 14 residues processed: 154 average time/residue: 1.6066 time to fit residues: 280.1991 Evaluate side-chains 141 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23834 Z= 0.274 Angle : 0.607 8.876 32223 Z= 0.298 Chirality : 0.042 0.193 3526 Planarity : 0.004 0.050 4112 Dihedral : 8.263 140.575 3252 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.49 % Allowed : 11.40 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2839 helix: 1.27 (0.15), residues: 1357 sheet: 0.47 (0.25), residues: 418 loop : 0.58 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 781 HIS 0.005 0.001 HIS A 418 PHE 0.023 0.001 PHE D 360 TYR 0.021 0.001 TYR A 787 ARG 0.005 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.3678 (m-80) cc_final: 0.3411 (m-80) REVERT: B 120 MET cc_start: 0.4013 (mtm) cc_final: 0.3402 (mmm) REVERT: A 715 MET cc_start: 0.1090 (mmt) cc_final: 0.0515 (mmt) REVERT: C 176 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7446 (mpt) REVERT: C 314 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: E 105 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7500 (ptp) REVERT: E 120 MET cc_start: 0.4963 (mtm) cc_final: 0.1547 (mmt) REVERT: D 371 MET cc_start: 0.8781 (mmm) cc_final: 0.8493 (mmp) REVERT: D 715 MET cc_start: 0.1454 (mpt) cc_final: 0.1088 (mmt) REVERT: F 72 GLU cc_start: 0.7466 (pm20) cc_final: 0.7149 (pm20) REVERT: G 355 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7514 (mmm) outliers start: 37 outliers final: 15 residues processed: 155 average time/residue: 1.5993 time to fit residues: 280.7761 Evaluate side-chains 145 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.0050 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23834 Z= 0.198 Angle : 0.581 8.885 32223 Z= 0.284 Chirality : 0.041 0.211 3526 Planarity : 0.003 0.044 4112 Dihedral : 8.088 135.380 3252 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.45 % Allowed : 11.89 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2839 helix: 1.36 (0.15), residues: 1340 sheet: 0.46 (0.25), residues: 415 loop : 0.55 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 781 HIS 0.006 0.001 HIS G 275 PHE 0.028 0.001 PHE A 360 TYR 0.025 0.001 TYR A 787 ARG 0.004 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4173 (mtm) cc_final: 0.3591 (mmm) REVERT: A 715 MET cc_start: 0.0943 (mmt) cc_final: 0.0268 (mmt) REVERT: C 176 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7438 (mpt) REVERT: C 299 MET cc_start: 0.8368 (mmp) cc_final: 0.7974 (mmt) REVERT: E 120 MET cc_start: 0.4841 (mtm) cc_final: 0.1493 (mmt) REVERT: D 371 MET cc_start: 0.8744 (mmm) cc_final: 0.8336 (mmt) REVERT: D 715 MET cc_start: 0.1459 (mpt) cc_final: 0.1113 (mmt) REVERT: F 72 GLU cc_start: 0.7464 (pm20) cc_final: 0.7190 (pm20) REVERT: G 184 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: G 314 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: G 355 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7470 (mmm) outliers start: 36 outliers final: 13 residues processed: 157 average time/residue: 1.6199 time to fit residues: 288.0824 Evaluate side-chains 143 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain G residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 111 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 78 optimal weight: 0.0870 chunk 231 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 270 optimal weight: 0.7980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23834 Z= 0.177 Angle : 0.593 9.475 32223 Z= 0.289 Chirality : 0.041 0.329 3526 Planarity : 0.003 0.044 4112 Dihedral : 7.938 130.385 3252 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.25 % Allowed : 12.25 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2839 helix: 1.38 (0.15), residues: 1355 sheet: 0.57 (0.26), residues: 395 loop : 0.55 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 781 HIS 0.006 0.001 HIS G 275 PHE 0.021 0.001 PHE A 360 TYR 0.025 0.001 TYR A 787 ARG 0.004 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 MET cc_start: 0.0918 (mmt) cc_final: 0.0257 (mmt) REVERT: C 176 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7394 (mpt) REVERT: C 299 MET cc_start: 0.8343 (mmp) cc_final: 0.7940 (mmt) REVERT: E 31 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7093 (tp40) REVERT: E 120 MET cc_start: 0.5083 (mtm) cc_final: 0.1758 (mmt) REVERT: D 371 MET cc_start: 0.8773 (mmm) cc_final: 0.8436 (mmp) REVERT: D 715 MET cc_start: 0.1451 (mpt) cc_final: 0.1127 (mmt) REVERT: F 72 GLU cc_start: 0.7429 (pm20) cc_final: 0.7188 (pm20) REVERT: G 184 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: G 314 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: G 355 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7477 (mmm) outliers start: 31 outliers final: 15 residues processed: 153 average time/residue: 1.6371 time to fit residues: 285.7895 Evaluate side-chains 146 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain G residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 174 optimal weight: 0.4980 chunk 138 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 overall best weight: 1.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 31 GLN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23834 Z= 0.268 Angle : 0.630 11.044 32223 Z= 0.306 Chirality : 0.042 0.216 3526 Planarity : 0.004 0.043 4112 Dihedral : 7.993 126.088 3252 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.01 % Allowed : 12.73 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2839 helix: 1.36 (0.15), residues: 1357 sheet: 0.42 (0.26), residues: 415 loop : 0.57 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 781 HIS 0.007 0.001 HIS G 275 PHE 0.017 0.001 PHE D 360 TYR 0.029 0.001 TYR A 787 ARG 0.004 0.000 ARG E 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4121 (mtm) cc_final: 0.3353 (mmm) REVERT: A 715 MET cc_start: 0.1073 (mmt) cc_final: 0.0407 (mmt) REVERT: C 176 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7505 (mpt) REVERT: C 299 MET cc_start: 0.8376 (mmp) cc_final: 0.8026 (mmt) REVERT: C 314 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: E 31 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7150 (tp40) REVERT: E 120 MET cc_start: 0.5056 (mtm) cc_final: 0.1720 (mmt) REVERT: D 371 MET cc_start: 0.8785 (mmm) cc_final: 0.8501 (tpp) REVERT: D 715 MET cc_start: 0.1503 (mpt) cc_final: 0.1194 (mmt) REVERT: F 72 GLU cc_start: 0.7518 (pm20) cc_final: 0.7262 (pm20) REVERT: G 184 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: G 314 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8167 (tt0) outliers start: 25 outliers final: 17 residues processed: 145 average time/residue: 1.5770 time to fit residues: 259.7040 Evaluate side-chains 146 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 783 MET Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.091557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057931 restraints weight = 78436.409| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.79 r_work: 0.2762 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 23834 Z= 0.322 Angle : 0.645 12.236 32223 Z= 0.313 Chirality : 0.043 0.211 3526 Planarity : 0.004 0.044 4112 Dihedral : 8.005 125.762 3252 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.21 % Allowed : 12.49 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2839 helix: 1.33 (0.15), residues: 1360 sheet: 0.38 (0.25), residues: 415 loop : 0.53 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 781 HIS 0.006 0.001 HIS G 275 PHE 0.020 0.001 PHE A 360 TYR 0.027 0.001 TYR A 787 ARG 0.004 0.000 ARG E 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7137.60 seconds wall clock time: 128 minutes 56.82 seconds (7736.82 seconds total)