Starting phenix.real_space_refine on Sun Feb 18 18:40:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whi_21517/02_2024/6whi_21517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whi_21517/02_2024/6whi_21517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whi_21517/02_2024/6whi_21517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whi_21517/02_2024/6whi_21517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whi_21517/02_2024/6whi_21517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whi_21517/02_2024/6whi_21517.pdb" } resolution = 4.2 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= 0.004 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: 5 Type Number sf(0) Gaussians P 109 5.49 5 S 15 5.16 5 C 13846 2.51 5 N 4080 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22636 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2187 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 302} Link IDs: {'PTRANS': 22, 'TRANS': 387} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1159 Unresolved non-hydrogen angles: 1483 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 32, 'ASP:plan': 21, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 12, 'GLU:plan': 29, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 732 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2129 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 22, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2111 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 103 Chain: "D" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2492 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2500 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2521 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2474 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2484 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 11, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 18, 'rna3p': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 920 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 159} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 378 Chain: "I" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 489 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 482 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 174 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' DG:plan': 4, ' DG:plan2': 4, ' DC:plan2': 3, ' DA:plan2': 5, ' DC:plan': 3, ' DT:plan': 3, ' DA:plan': 5} Unresolved non-hydrogen planarities: 160 Chain: "Q" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' DG:plan': 4, ' DG:plan2': 4, ' DC:plan2': 3, ' DA:plan2': 2, ' DC:plan': 3, ' DT:plan': 1, ' DA:plan': 2} Unresolved non-hydrogen planarities: 109 Chain: "P" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 114 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' DG:plan': 3, ' DG:plan2': 3, ' DC:plan2': 4, ' DA:plan2': 1, ' DC:plan': 4, ' DT:plan': 2, ' DA:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "O" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 171 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {' DG:plan': 3, ' DG:plan2': 3, ' DC:plan2': 4, ' DA:plan2': 3, ' DC:plan': 4, ' DT:plan': 5, ' DA:plan': 3} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 13.31, per 1000 atoms: 0.59 Number of scatterers: 22636 At special positions: 0 Unit cell: (138, 139.15, 154.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 109 15.00 O 4586 8.00 N 4080 7.00 C 13846 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: 9.60 Conformation dependent library (CDL) restraints added in 4.6 seconds 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5524 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 41 sheets defined 34.8% alpha, 20.7% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 7.76 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 removed outlier: 4.339A pdb=" N SER A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 removed outlier: 4.510A pdb=" N LYS A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 49 Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.726A pdb=" N ALA A 56 " --> pdb=" O TRP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.879A pdb=" N ALA A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 162 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.878A pdb=" N PHE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 314 through 342 removed outlier: 3.737A pdb=" N ARG A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.975A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.909A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.596A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 181 removed outlier: 3.888A pdb=" N ARG B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.772A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.029A pdb=" N ASP C 53 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER C 55 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 148 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 208 through 224 Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.779A pdb=" N ALA C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.815A pdb=" N SER C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.507A pdb=" N ARG D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.887A pdb=" N ALA D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.738A pdb=" N SER D 306 " --> pdb=" O PRO D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 49 through 54 removed outlier: 4.150A pdb=" N ASP E 53 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 Processing helix chain 'E' and resid 130 through 148 removed outlier: 3.560A pdb=" N ARG E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 163 Processing helix chain 'E' and resid 208 through 224 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.698A pdb=" N ALA E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.074A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.153A pdb=" N ASP F 53 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 91 Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.513A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 208 through 224 Processing helix chain 'F' and resid 275 through 284 removed outlier: 3.692A pdb=" N ALA F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.735A pdb=" N SER F 306 " --> pdb=" O PRO F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 49 through 54 removed outlier: 4.161A pdb=" N ASP G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.568A pdb=" N ASP G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 removed outlier: 3.585A pdb=" N ARG G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 208 through 224 Processing helix chain 'G' and resid 275 through 284 removed outlier: 3.603A pdb=" N ALA G 282 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 306 removed outlier: 3.910A pdb=" N SER G 306 " --> pdb=" O PRO G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 333 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 48 through 53 removed outlier: 4.526A pdb=" N ASP H 53 " --> pdb=" O TRP H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'H' and resid 208 through 224 Processing helix chain 'H' and resid 275 through 284 removed outlier: 3.573A pdb=" N ALA H 282 " --> pdb=" O LYS H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 306 removed outlier: 3.715A pdb=" N SER H 306 " --> pdb=" O PRO H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 333 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'L' and resid 16 through 33 removed outlier: 3.601A pdb=" N GLN L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 73 removed outlier: 3.752A pdb=" N ALA L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 121 removed outlier: 3.716A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 131 Processing helix chain 'L' and resid 132 through 136 removed outlier: 3.914A pdb=" N ALA L 136 " --> pdb=" O ASP L 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'J' and resid 26 through 37 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.863A pdb=" N ASP A 107 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.618A pdb=" N ALA A 95 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 3.554A pdb=" N SER B 143 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 251 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 190 removed outlier: 6.769A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.914A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 240 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.665A pdb=" N TRP B 29 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 306 through 307 Processing sheet with id=AA9, first strand: chain 'C' and resid 127 through 128 removed outlier: 3.956A pdb=" N ALA C 127 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 31 " --> pdb=" O PHE C 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.636A pdb=" N ASP C 38 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG C 117 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189 removed outlier: 4.581A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 272 " --> pdb=" O MET C 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.770A pdb=" N THR C 264 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 128 removed outlier: 3.807A pdb=" N ALA D 127 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 32 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 31 " --> pdb=" O PHE D 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.728A pdb=" N ARG D 117 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 118 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 188 through 189 removed outlier: 4.538A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 118 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA D 272 " --> pdb=" O MET D 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 64 through 70 removed outlier: 3.554A pdb=" N ARG D 64 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER D 262 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR D 97 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR D 264 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP D 99 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 127 through 128 removed outlier: 4.140A pdb=" N ALA E 127 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 32 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU E 31 " --> pdb=" O PHE E 355 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.763A pdb=" N ARG E 117 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.763A pdb=" N ARG E 117 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA E 272 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 64 through 69 removed outlier: 3.508A pdb=" N VAL E 98 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 64 through 69 removed outlier: 3.508A pdb=" N VAL E 98 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN E 260 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.874A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 32 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE F 33 " --> pdb=" O GLY F 353 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY F 353 " --> pdb=" O PHE F 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.645A pdb=" N ASP F 38 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 117 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 231 " --> pdb=" O ASN F 182 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.645A pdb=" N ASP F 38 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 117 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA F 272 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 64 through 70 removed outlier: 3.580A pdb=" N GLN F 96 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 248 through 249 removed outlier: 3.796A pdb=" N THR F 264 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 128 removed outlier: 3.843A pdb=" N ALA G 127 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 32 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU G 31 " --> pdb=" O PHE G 355 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.703A pdb=" N ASP G 38 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU G 231 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 188 through 189 removed outlier: 3.587A pdb=" N GLU G 231 " --> pdb=" O ASN G 182 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.628A pdb=" N VAL G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.628A pdb=" N VAL G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR G 97 " --> pdb=" O SER G 262 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR G 264 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP G 99 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR G 264 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.817A pdb=" N ALA H 127 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 32 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU H 31 " --> pdb=" O PHE H 355 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.531A pdb=" N ASP H 38 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG H 117 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL H 179 " --> pdb=" O PHE H 195 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.531A pdb=" N ASP H 38 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG H 117 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA H 272 " --> pdb=" O MET H 44 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 64 through 70 removed outlier: 4.884A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 41 through 43 removed outlier: 3.823A pdb=" N ALA L 62 " --> pdb=" O HIS L 3 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS L 3 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AE2, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=AE3, first strand: chain 'L' and resid 146 through 148 removed outlier: 5.315A pdb=" N SER L 148 " --> pdb=" O GLN L 153 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN L 153 " --> pdb=" O SER L 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 20 through 21 removed outlier: 3.638A pdb=" N VAL I 20 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER I 49 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP I 54 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 20 through 21 removed outlier: 6.529A pdb=" N SER J 49 " --> pdb=" O TRP J 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP J 54 " --> pdb=" O SER J 49 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 7.92 Time building geometry restraints manager: 10.11 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: 3686 1.31 - 1.43: 6203 1.43 - 1.56: 13062 1.56 - 1.68: 214 1.68 - 1.80: 22 Bond restraints: 23187 Sorted by residual: bond pdb=" C ALA E 300 " pdb=" N VAL E 301 " ideal model delta sigma weight residual 1.333 1.260 0.073 1.20e-02 6.94e+03 3.66e+01 bond pdb=" C ARG E 315 " pdb=" O ARG E 315 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.26e-02 6.30e+03 1.88e+01 bond pdb=" N PRO A 269 " pdb=" CD PRO A 269 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta sigma weight residual 1.467 1.420 0.047 1.21e-02 6.83e+03 1.49e+01 bond pdb=" CA VAL E 301 " pdb=" CB VAL E 301 " ideal model delta sigma weight residual 1.536 1.491 0.045 1.16e-02 7.43e+03 1.48e+01 ... (remaining 23182 not shown) Histogram of bond angle deviations from ideal: 90.37 - 99.15: 7 99.15 - 107.93: 1795 107.93 - 116.71: 15089 116.71 - 125.49: 14613 125.49 - 134.26: 526 Bond angle restraints: 32030 Sorted by residual: angle pdb=" N LEU A 94 " pdb=" CA LEU A 94 " pdb=" C LEU A 94 " ideal model delta sigma weight residual 109.07 90.37 18.70 1.52e+00 4.33e-01 1.51e+02 angle pdb=" N TYR A 187 " pdb=" CA TYR A 187 " pdb=" C TYR A 187 " ideal model delta sigma weight residual 110.53 124.16 -13.63 1.32e+00 5.74e-01 1.07e+02 angle pdb=" N LEU A 104 " pdb=" CA LEU A 104 " pdb=" C LEU A 104 " ideal model delta sigma weight residual 109.15 95.33 13.82 1.44e+00 4.82e-01 9.21e+01 angle pdb=" C ALA E 300 " pdb=" N VAL E 301 " pdb=" CA VAL E 301 " ideal model delta sigma weight residual 120.98 108.38 12.60 1.36e+00 5.41e-01 8.58e+01 angle pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" CD PRO A 266 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.34e+01 ... (remaining 32025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 13315 21.12 - 42.24: 384 42.24 - 63.37: 196 63.37 - 84.49: 44 84.49 - 105.61: 5 Dihedral angle restraints: 13944 sinusoidal: 5409 harmonic: 8535 Sorted by residual: dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 102.74 97.26 1 1.50e+01 4.44e-03 4.81e+01 dihedral pdb=" O4' U M 2 " pdb=" C1' U M 2 " pdb=" N1 U M 2 " pdb=" C2 U M 2 " ideal model delta sinusoidal sigma weight residual -128.00 -38.81 -89.19 1 1.70e+01 3.46e-03 3.27e+01 dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual -160.00 -94.55 -65.45 1 1.50e+01 4.44e-03 2.49e+01 ... (remaining 13941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3652 0.111 - 0.223: 179 0.223 - 0.334: 19 0.334 - 0.445: 2 0.445 - 0.557: 1 Chirality restraints: 3853 Sorted by residual: chirality pdb=" C3' U M 10 " pdb=" C4' U M 10 " pdb=" O3' U M 10 " pdb=" C2' U M 10 " both_signs ideal model delta sigma weight residual False -2.48 -1.92 -0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" CA ASP H 256 " pdb=" N ASP H 256 " pdb=" C ASP H 256 " pdb=" CB ASP H 256 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C1' G M 26 " pdb=" O4' G M 26 " pdb=" C2' G M 26 " pdb=" N9 G M 26 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 3850 not shown) Planarity restraints: 3906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 265 " -0.123 5.00e-02 4.00e+02 1.74e-01 4.83e+01 pdb=" N PRO A 266 " 0.300 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U M 10 " -0.045 2.00e-02 2.50e+03 3.57e-02 2.86e+01 pdb=" N1 U M 10 " 0.088 2.00e-02 2.50e+03 pdb=" C2 U M 10 " -0.037 2.00e-02 2.50e+03 pdb=" O2 U M 10 " 0.010 2.00e-02 2.50e+03 pdb=" N3 U M 10 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U M 10 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U M 10 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U M 10 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U M 10 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 301 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.53e+01 pdb=" C VAL E 301 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL E 301 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU E 302 " 0.023 2.00e-02 2.50e+03 ... (remaining 3903 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 217 2.52 - 3.12: 17764 3.12 - 3.71: 33199 3.71 - 4.31: 44959 4.31 - 4.90: 76228 Nonbonded interactions: 172367 Sorted by model distance: nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 1.927 2.440 nonbonded pdb=" OG SER B 143 " pdb=" OD2 ASP H 38 " model vdw 1.957 2.440 nonbonded pdb=" O ARG G 69 " pdb=" O2' G M 19 " model vdw 1.962 2.440 nonbonded pdb=" O2' G M 18 " pdb=" O4' G M 19 " model vdw 1.971 2.440 nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 1.987 2.440 ... (remaining 172362 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 'C' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 190 or (resid 191 through 192 and \ (name N or name CA or name C or name O or name CB )) or resid 193 through 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 8 through 285 or (resid 286 and (name N or name CA or name C or name O or name C \ B )) or resid 287 through 295 or (resid 296 and (name N or name CA or name C or \ name O or name CB )) or resid 297 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 356)) selection = (chain 'D' and (resid 25 through 50 or (resid 51 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 and (na \ me N or name CA or name C or name O or name CB )) or resid 65 through 66 or resi \ d 98 through 104 or (resid 105 through 107 and (name N or name CA or name C or n \ ame O or name CB )) or resid 108 through 145 or (resid 146 through 147 and (name \ N or name CA or name C or name O or name CB )) or resid 148 through 151 or (res \ id 152 and (name N or name CA or name C or name O or name CB )) or resid 153 thr \ ough 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) \ or resid 170 through 174 or (resid 175 through 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 184 or (resid 185 through 186 a \ nd (name N or name CA or name C or name O or name CB )) or resid 187 or (resid 1 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 189 through \ 190 or (resid 191 through 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 195 or (resid 196 through 199 and (name N or name C \ A or name C or name O or name CB )) or resid 200 through 201 or (resid 202 throu \ gh 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 209 or (resid 210 and (name N or name CA or name C or name \ O or name CB )) or resid 211 through 226 or (resid 227 and (name N or name CA or \ name C or name O or name CB )) or resid 228 through 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 249 or (res \ id 250 and (name N or name CA or name C or name O or name CB )) or resid 263 thr \ ough 268 or (resid 269 through 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 through 303 or (resid 304 and (name N or name CA or nam \ e C or name O or name CB )) or resid 305 through 311 or (resid 312 through 313 a \ nd (name N or name CA or name C or name O or name CB )) or resid 314 through 317 \ or (resid 318 and (name N or name CA or name C or name O or name CB )) or resid \ 319 or (resid 320 through 322 and (name N or name CA or name C or name O or nam \ e CB )) or resid 323 through 339 or (resid 340 and (name N or name CA or name C \ or name O or name CB )) or resid 341 through 356)) selection = (chain 'E' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 295 or (resid 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 311 or (resid 312 \ through 313 and (name N or name CA or name C or name O or name CB )) or resid 31 \ 4 through 317 or (resid 318 and (name N or name CA or name C or name O or name C \ B )) or resid 319 or (resid 320 through 322 and (name N or name CA or name C or \ name O or name CB )) or resid 323 through 339 or (resid 340 and (name N or name \ CA or name C or name O or name CB )) or resid 341 through 356)) selection = (chain 'F' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 295 or (resid 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 303 or (resid 304 \ and (name N or name CA or name C or name O or name CB )) or resid 305 through 31 \ 1 or (resid 312 through 313 and (name N or name CA or name C or name O or name C \ B )) or resid 314 through 317 or (resid 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 or (resid 320 through 322 and (name N or name \ CA or name C or name O or name CB )) or resid 323 through 339 or (resid 340 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 356)) selection = (chain 'G' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 190 or (resid 191 through 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (name N \ or name CA or name C or name O or name CB )) or resid 200 through 201 or (resid \ 202 through 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 or (resid 206 through 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N or n \ ame CA or name C or name O or name CB )) or resid 228 through 239 or (resid 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 9 or (resid 250 and (name N or name CA or name C or name O or name CB )) or resi \ d 263 through 268 or (resid 269 through 273 and (name N or name CA or name C or \ name O or name CB )) or resid 274 through 285 or (resid 286 and (name N or name \ CA or name C or name O or name CB )) or resid 287 through 295 or (resid 296 and \ (name N or name CA or name C or name O or name CB )) or resid 297 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 5 through 311 or (resid 312 through 313 and (name N or name CA or name C or name \ O or name CB )) or resid 314 through 317 or (resid 318 and (name N or name CA o \ r name C or name O or name CB )) or resid 319 or (resid 320 through 322 and (nam \ e N or name CA or name C or name O or name CB )) or resid 323 through 339 or (re \ sid 340 and (name N or name CA or name C or name O or name CB )) or resid 341 th \ rough 356)) selection = (chain 'H' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 195 or (resid 196 through 199 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 201 or (resid 202 through 204 and (nam \ e N or name CA or name C or name O or name CB )) or resid 205 or (resid 206 thro \ ugh 207 and (name N or name CA or name C or name O or name CB )) or resid 208 th \ rough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 211 through 239 or (resid 240 and (name N or name CA or name C or name \ O or name CB )) or resid 241 through 249 or (resid 250 and (name N or name CA o \ r name C or name O or name CB )) or resid 263 through 268 or (resid 269 through \ 273 and (name N or name CA or name C or name O or name CB )) or resid 274 throug \ h 303 or (resid 304 and (name N or name CA or name C or name O or name CB )) or \ resid 305 through 311 or (resid 312 through 313 and (name N or name CA or name C \ or name O or name CB )) or resid 314 through 317 or (resid 318 and (name N or n \ ame CA or name C or name O or name CB )) or resid 319 through 320 or (resid 321 \ through 322 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 3 through 339 or (resid 340 and (name N or name CA or name C or name O or name C \ B )) or resid 341 through 356)) } ncs_group { reference = (chain 'I' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 36 or (resid 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 through 52 or (resid 53 and (n \ ame N or name CA or name C or name O or name CB )) or resid 54 through 58 or (re \ sid 59 through 60 and (name N or name CA or name C or name O or name CB )) or re \ sid 61 through 66)) selection = (chain 'J' and (resid 3 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 66)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 3.170 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 66.990 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.005 0.073 23187 Z= 0.358 Angle : 0.947 18.698 32030 Z= 0.625 Chirality : 0.056 0.557 3853 Planarity : 0.005 0.174 3906 Dihedral : 13.261 105.611 8420 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -1.63 (0.14), residues: 2930 helix: 0.67 (0.18), residues: 891 sheet: -1.10 (0.22), residues: 415 loop : -2.19 (0.13), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 193 HIS 0.008 0.002 HIS B 306 PHE 0.028 0.002 PHE E 166 TYR 0.019 0.002 TYR D 290 ARG 0.022 0.001 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 651 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 LEU cc_start: 0.5591 (mt) cc_final: 0.5026 (pp) REVERT: B 125 GLU cc_start: 0.7099 (tp30) cc_final: 0.6670 (tm-30) REVERT: C 168 TRP cc_start: 0.8171 (m100) cc_final: 0.7890 (m100) REVERT: D 109 THR cc_start: 0.9049 (m) cc_final: 0.8312 (p) REVERT: D 143 THR cc_start: 0.8397 (m) cc_final: 0.8084 (m) REVERT: D 348 ASN cc_start: 0.8426 (t0) cc_final: 0.8008 (t0) REVERT: E 76 LEU cc_start: 0.7500 (mp) cc_final: 0.7081 (mt) REVERT: E 208 ASP cc_start: 0.6778 (t0) cc_final: 0.6428 (m-30) REVERT: E 287 ASP cc_start: 0.7076 (t0) cc_final: 0.6491 (t0) REVERT: E 299 ILE cc_start: 0.9125 (mt) cc_final: 0.8837 (mt) REVERT: F 194 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7497 (mtp180) REVERT: F 321 LEU cc_start: 0.7250 (mt) cc_final: 0.6927 (mt) REVERT: G 102 ASN cc_start: 0.8567 (m-40) cc_final: 0.8144 (m-40) REVERT: G 233 VAL cc_start: 0.9337 (t) cc_final: 0.9130 (m) REVERT: G 245 PHE cc_start: 0.8741 (m-80) cc_final: 0.8287 (m-80) REVERT: G 354 VAL cc_start: 0.8756 (t) cc_final: 0.8544 (p) REVERT: H 175 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7560 (mt-10) REVERT: H 287 ASP cc_start: 0.8265 (t0) cc_final: 0.7954 (t0) REVERT: H 290 TYR cc_start: 0.5689 (p90) cc_final: 0.5124 (p90) REVERT: H 322 ASP cc_start: 0.7012 (t0) cc_final: 0.6558 (t70) REVERT: I 54 TRP cc_start: 0.7635 (m-10) cc_final: 0.7389 (m-10) REVERT: J 49 SER cc_start: 0.8762 (p) cc_final: 0.8457 (m) REVERT: J 64 TRP cc_start: 0.8789 (m100) cc_final: 0.7680 (m100) outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.4170 time to fit residues: 402.3071 Evaluate side-chains 322 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 188 HIS A 230 HIS B 45 GLN C 148 GLN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 227 HIS D 310 GLN D 343 HIS ** E 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 102 ASN F 170 ASN F 281 ASN F 310 GLN F 319 GLN G 348 ASN I 12 ASN J 12 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23187 Z= 0.265 Angle : 0.599 9.985 32030 Z= 0.319 Chirality : 0.042 0.290 3853 Planarity : 0.005 0.068 3906 Dihedral : 15.147 117.617 4592 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: -0.43 (0.15), residues: 2930 helix: 1.66 (0.18), residues: 921 sheet: -0.33 (0.21), residues: 480 loop : -1.56 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 228 HIS 0.007 0.002 HIS F 343 PHE 0.017 0.002 PHE D 245 TYR 0.018 0.002 TYR E 290 ARG 0.011 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8030 (mt) cc_final: 0.7819 (mt) REVERT: B 86 ASN cc_start: 0.8583 (m-40) cc_final: 0.8377 (m-40) REVERT: B 125 GLU cc_start: 0.7089 (tp30) cc_final: 0.6671 (tm-30) REVERT: B 194 GLN cc_start: 0.8364 (tp40) cc_final: 0.8010 (tp40) REVERT: C 58 TRP cc_start: 0.8488 (m-10) cc_final: 0.8175 (m-10) REVERT: C 163 ASN cc_start: 0.8162 (p0) cc_final: 0.7681 (p0) REVERT: C 310 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 348 ASN cc_start: 0.8907 (t0) cc_final: 0.8636 (t0) REVERT: D 109 THR cc_start: 0.9060 (m) cc_final: 0.8166 (p) REVERT: D 147 ASP cc_start: 0.7755 (m-30) cc_final: 0.7540 (m-30) REVERT: D 160 ASN cc_start: 0.8689 (m-40) cc_final: 0.8455 (m-40) REVERT: D 242 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7925 (mm-40) REVERT: D 321 LEU cc_start: 0.7912 (mt) cc_final: 0.7593 (mp) REVERT: E 49 TRP cc_start: 0.9209 (t-100) cc_final: 0.8522 (t-100) REVERT: E 62 THR cc_start: 0.8699 (p) cc_final: 0.8419 (t) REVERT: E 130 ASP cc_start: 0.8430 (t0) cc_final: 0.7878 (m-30) REVERT: E 242 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8890 (mm-40) REVERT: F 102 ASN cc_start: 0.8932 (m110) cc_final: 0.8463 (m-40) REVERT: F 146 ASN cc_start: 0.8516 (t0) cc_final: 0.8266 (t0) REVERT: F 225 SER cc_start: 0.9027 (m) cc_final: 0.8456 (p) REVERT: G 195 PHE cc_start: 0.8636 (m-10) cc_final: 0.8356 (m-10) REVERT: G 354 VAL cc_start: 0.8993 (t) cc_final: 0.8773 (p) REVERT: H 102 ASN cc_start: 0.8479 (m-40) cc_final: 0.8109 (m-40) REVERT: H 124 THR cc_start: 0.9325 (t) cc_final: 0.9086 (p) REVERT: H 245 PHE cc_start: 0.8360 (m-80) cc_final: 0.7626 (m-10) REVERT: I 54 TRP cc_start: 0.8308 (m-10) cc_final: 0.8104 (m-10) REVERT: J 44 VAL cc_start: 0.9422 (m) cc_final: 0.9153 (p) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.3296 time to fit residues: 219.1179 Evaluate side-chains 273 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 274 optimal weight: 40.0000 chunk 296 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 272 optimal weight: 0.0570 chunk 93 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A 230 HIS B 45 GLN B 104 HIS D 94 ASN D 248 GLN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN F 343 HIS ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN H 96 GLN H 159 HIS H 310 GLN I 11 GLN J 12 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23187 Z= 0.293 Angle : 0.574 7.906 32030 Z= 0.310 Chirality : 0.040 0.254 3853 Planarity : 0.005 0.079 3906 Dihedral : 15.176 120.606 4592 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.11 % Allowed : 3.73 % Favored : 96.16 % 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: -0.28 (0.15), residues: 2930 helix: 1.67 (0.18), residues: 924 sheet: 0.16 (0.21), residues: 500 loop : -1.58 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 49 HIS 0.011 0.001 HIS G 227 PHE 0.019 0.002 PHE G 245 TYR 0.024 0.002 TYR H 344 ARG 0.009 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 395 time to evaluate : 2.819 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 193 LEU cc_start: 0.8072 (mt) cc_final: 0.7839 (mt) REVERT: B 125 GLU cc_start: 0.7509 (tp30) cc_final: 0.6874 (tm-30) REVERT: B 304 TYR cc_start: 0.6986 (m-10) cc_final: 0.6759 (m-10) REVERT: C 310 GLN cc_start: 0.8708 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 348 ASN cc_start: 0.9098 (t0) cc_final: 0.8776 (t0) REVERT: D 74 ASN cc_start: 0.9063 (p0) cc_final: 0.8767 (p0) REVERT: D 76 LEU cc_start: 0.8114 (tp) cc_final: 0.7799 (mt) REVERT: D 160 ASN cc_start: 0.8518 (m-40) cc_final: 0.8231 (m-40) REVERT: D 242 GLN cc_start: 0.8557 (tp-100) cc_final: 0.7926 (mm-40) REVERT: D 277 GLN cc_start: 0.8914 (pm20) cc_final: 0.8687 (pm20) REVERT: D 321 LEU cc_start: 0.8204 (mt) cc_final: 0.7744 (mp) REVERT: E 49 TRP cc_start: 0.9325 (t-100) cc_final: 0.8765 (t-100) REVERT: E 62 THR cc_start: 0.8705 (p) cc_final: 0.8383 (t) REVERT: E 130 ASP cc_start: 0.8348 (t0) cc_final: 0.7798 (m-30) REVERT: E 189 VAL cc_start: 0.9368 (t) cc_final: 0.9107 (m) REVERT: E 212 ASP cc_start: 0.8604 (m-30) cc_final: 0.8110 (t0) REVERT: F 34 GLU cc_start: 0.8081 (tt0) cc_final: 0.7866 (tt0) REVERT: F 102 ASN cc_start: 0.8986 (m110) cc_final: 0.7943 (m-40) REVERT: F 177 VAL cc_start: 0.9408 (t) cc_final: 0.9192 (m) REVERT: F 202 LEU cc_start: 0.8317 (tp) cc_final: 0.8034 (tt) REVERT: F 277 GLN cc_start: 0.9007 (pm20) cc_final: 0.8508 (pm20) REVERT: G 94 ASN cc_start: 0.8581 (p0) cc_final: 0.8260 (p0) REVERT: G 106 ASP cc_start: 0.7925 (p0) cc_final: 0.7465 (p0) REVERT: G 109 THR cc_start: 0.9110 (m) cc_final: 0.8567 (p) REVERT: G 195 PHE cc_start: 0.8769 (m-10) cc_final: 0.8456 (m-10) REVERT: G 242 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8561 (mm-40) REVERT: G 315 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8333 (ttp-170) REVERT: H 87 ASP cc_start: 0.8259 (m-30) cc_final: 0.8028 (m-30) REVERT: H 102 ASN cc_start: 0.8445 (m-40) cc_final: 0.8217 (m-40) REVERT: H 269 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7297 (mtm-85) REVERT: H 302 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7348 (mm-30) REVERT: H 314 TYR cc_start: 0.8496 (m-80) cc_final: 0.8177 (m-80) REVERT: H 332 LEU cc_start: 0.8789 (mt) cc_final: 0.8511 (mt) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.3374 time to fit residues: 212.6265 Evaluate side-chains 265 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 30.0000 chunk 206 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 275 optimal weight: 50.0000 chunk 291 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 237 ASN D 96 GLN D 348 ASN ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN H 96 GLN H 183 HIS H 329 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23187 Z= 0.342 Angle : 0.597 8.879 32030 Z= 0.322 Chirality : 0.041 0.205 3853 Planarity : 0.004 0.081 3906 Dihedral : 15.221 116.799 4592 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 2930 helix: 1.51 (0.18), residues: 940 sheet: 0.18 (0.22), residues: 513 loop : -1.72 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 316 HIS 0.007 0.001 HIS B 306 PHE 0.028 0.002 PHE D 245 TYR 0.023 0.002 TYR E 290 ARG 0.011 0.001 ARG H 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9539 (m-40) cc_final: 0.9278 (m110) REVERT: B 54 ILE cc_start: 0.6937 (mp) cc_final: 0.6724 (mp) REVERT: B 82 ASN cc_start: 0.8648 (m110) cc_final: 0.8342 (m-40) REVERT: B 125 GLU cc_start: 0.7869 (tp30) cc_final: 0.7168 (tm-30) REVERT: C 238 ILE cc_start: 0.9263 (mm) cc_final: 0.8897 (tt) REVERT: C 310 GLN cc_start: 0.8683 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 348 ASN cc_start: 0.9214 (t0) cc_final: 0.8857 (t0) REVERT: D 74 ASN cc_start: 0.9022 (p0) cc_final: 0.8632 (p0) REVERT: D 160 ASN cc_start: 0.8529 (m-40) cc_final: 0.8298 (m-40) REVERT: D 206 LYS cc_start: 0.8677 (mppt) cc_final: 0.8433 (mttt) REVERT: D 242 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8020 (mm-40) REVERT: D 277 GLN cc_start: 0.8956 (pm20) cc_final: 0.8692 (pm20) REVERT: D 314 TYR cc_start: 0.8797 (m-80) cc_final: 0.8496 (m-10) REVERT: E 49 TRP cc_start: 0.9385 (t-100) cc_final: 0.8786 (t-100) REVERT: E 62 THR cc_start: 0.8840 (p) cc_final: 0.8506 (t) REVERT: E 124 THR cc_start: 0.9507 (m) cc_final: 0.9038 (p) REVERT: E 130 ASP cc_start: 0.8440 (t0) cc_final: 0.7911 (m-30) REVERT: E 189 VAL cc_start: 0.9383 (t) cc_final: 0.9080 (m) REVERT: E 212 ASP cc_start: 0.8666 (m-30) cc_final: 0.8203 (t0) REVERT: E 299 ILE cc_start: 0.8109 (pt) cc_final: 0.7659 (pt) REVERT: F 34 GLU cc_start: 0.7528 (tt0) cc_final: 0.7325 (tt0) REVERT: F 202 LEU cc_start: 0.8560 (tp) cc_final: 0.8359 (tt) REVERT: F 277 GLN cc_start: 0.9064 (pm20) cc_final: 0.8679 (pm20) REVERT: G 94 ASN cc_start: 0.8651 (p0) cc_final: 0.8442 (p0) REVERT: G 106 ASP cc_start: 0.8109 (p0) cc_final: 0.7768 (p0) REVERT: G 109 THR cc_start: 0.8968 (m) cc_final: 0.8344 (p) REVERT: H 87 ASP cc_start: 0.8333 (m-30) cc_final: 0.8126 (m-30) REVERT: H 102 ASN cc_start: 0.8520 (m-40) cc_final: 0.7977 (m-40) REVERT: H 269 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7323 (mtm-85) REVERT: I 6 ILE cc_start: 0.9167 (mt) cc_final: 0.8576 (tp) REVERT: I 11 GLN cc_start: 0.8386 (tp40) cc_final: 0.8076 (tm-30) REVERT: I 24 THR cc_start: 0.8771 (t) cc_final: 0.8527 (t) REVERT: I 43 THR cc_start: 0.9487 (p) cc_final: 0.8934 (t) REVERT: I 57 TYR cc_start: 0.9127 (p90) cc_final: 0.8812 (p90) outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.3083 time to fit residues: 168.2516 Evaluate side-chains 252 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 217 optimal weight: 0.0470 chunk 120 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 348 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN H 159 HIS ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23187 Z= 0.297 Angle : 0.554 7.820 32030 Z= 0.299 Chirality : 0.040 0.229 3853 Planarity : 0.004 0.042 3906 Dihedral : 15.143 116.661 4592 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: -0.29 (0.15), residues: 2930 helix: 1.67 (0.18), residues: 930 sheet: 0.31 (0.23), residues: 496 loop : -1.67 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 228 HIS 0.006 0.001 HIS G 227 PHE 0.017 0.002 PHE F 166 TYR 0.021 0.002 TYR H 344 ARG 0.006 0.001 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9552 (m-40) cc_final: 0.9318 (m110) REVERT: B 17 ILE cc_start: 0.8852 (mt) cc_final: 0.8496 (pt) REVERT: B 125 GLU cc_start: 0.7885 (tp30) cc_final: 0.7181 (tm-30) REVERT: B 288 GLU cc_start: 0.7412 (tt0) cc_final: 0.7211 (tt0) REVERT: C 58 TRP cc_start: 0.8980 (m-10) cc_final: 0.8485 (m-10) REVERT: C 168 TRP cc_start: 0.8391 (m100) cc_final: 0.8043 (m-10) REVERT: C 238 ILE cc_start: 0.9284 (mm) cc_final: 0.9007 (tt) REVERT: C 310 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 348 ASN cc_start: 0.9201 (t0) cc_final: 0.8593 (t0) REVERT: D 72 ILE cc_start: 0.9530 (mt) cc_final: 0.9289 (mm) REVERT: D 74 ASN cc_start: 0.9030 (p0) cc_final: 0.8637 (p0) REVERT: D 160 ASN cc_start: 0.8631 (m-40) cc_final: 0.8428 (m-40) REVERT: D 202 LEU cc_start: 0.8636 (tp) cc_final: 0.8236 (tt) REVERT: D 242 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8193 (mm-40) REVERT: D 277 GLN cc_start: 0.8968 (pm20) cc_final: 0.8744 (pm20) REVERT: D 314 TYR cc_start: 0.8730 (m-80) cc_final: 0.7997 (m-10) REVERT: E 62 THR cc_start: 0.8811 (p) cc_final: 0.8518 (t) REVERT: E 106 ASP cc_start: 0.7911 (p0) cc_final: 0.7645 (p0) REVERT: E 124 THR cc_start: 0.9529 (m) cc_final: 0.9135 (p) REVERT: E 130 ASP cc_start: 0.8410 (t0) cc_final: 0.7889 (m-30) REVERT: E 212 ASP cc_start: 0.8665 (m-30) cc_final: 0.8381 (t0) REVERT: E 287 ASP cc_start: 0.7778 (p0) cc_final: 0.7290 (p0) REVERT: E 354 VAL cc_start: 0.9150 (t) cc_final: 0.8901 (p) REVERT: F 34 GLU cc_start: 0.7684 (tt0) cc_final: 0.7477 (tt0) REVERT: F 202 LEU cc_start: 0.8555 (tp) cc_final: 0.8329 (tt) REVERT: F 245 PHE cc_start: 0.8919 (m-80) cc_final: 0.8697 (m-80) REVERT: F 261 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8776 (mtpt) REVERT: F 277 GLN cc_start: 0.9034 (pm20) cc_final: 0.8660 (pm20) REVERT: G 106 ASP cc_start: 0.8067 (p0) cc_final: 0.7582 (p0) REVERT: G 109 THR cc_start: 0.8895 (m) cc_final: 0.8288 (p) REVERT: H 87 ASP cc_start: 0.8399 (m-30) cc_final: 0.8101 (m-30) REVERT: H 124 THR cc_start: 0.9451 (t) cc_final: 0.9195 (p) REVERT: H 269 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7335 (mtm-85) REVERT: H 322 ASP cc_start: 0.8128 (t70) cc_final: 0.7830 (t0) REVERT: I 6 ILE cc_start: 0.9149 (mt) cc_final: 0.8643 (tp) REVERT: I 11 GLN cc_start: 0.8226 (tp40) cc_final: 0.7794 (tp-100) REVERT: I 24 THR cc_start: 0.8703 (t) cc_final: 0.8469 (t) REVERT: I 43 THR cc_start: 0.9422 (p) cc_final: 0.8868 (t) REVERT: J 11 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7584 (tp40) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2896 time to fit residues: 159.1154 Evaluate side-chains 250 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 171 optimal weight: 0.0670 chunk 72 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS C 227 HIS D 94 ASN D 170 ASN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 348 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 HIS ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23187 Z= 0.228 Angle : 0.516 9.951 32030 Z= 0.275 Chirality : 0.039 0.236 3853 Planarity : 0.004 0.038 3906 Dihedral : 15.058 114.986 4592 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.13 (0.15), residues: 2930 helix: 1.86 (0.18), residues: 926 sheet: 0.47 (0.24), residues: 481 loop : -1.60 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 316 HIS 0.008 0.001 HIS G 227 PHE 0.016 0.002 PHE D 245 TYR 0.021 0.002 TYR D 344 ARG 0.004 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9573 (m-40) cc_final: 0.9359 (m110) REVERT: B 17 ILE cc_start: 0.8885 (mt) cc_final: 0.8538 (pt) REVERT: B 102 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7408 (mmm-85) REVERT: B 125 GLU cc_start: 0.7822 (tp30) cc_final: 0.7140 (tm-30) REVERT: C 58 TRP cc_start: 0.8936 (m-10) cc_final: 0.8528 (m-10) REVERT: C 168 TRP cc_start: 0.8318 (m100) cc_final: 0.7986 (m100) REVERT: C 238 ILE cc_start: 0.9252 (mm) cc_final: 0.8943 (tt) REVERT: C 334 ASP cc_start: 0.8901 (m-30) cc_final: 0.8665 (m-30) REVERT: C 348 ASN cc_start: 0.9160 (t0) cc_final: 0.8348 (t0) REVERT: D 72 ILE cc_start: 0.9543 (mt) cc_final: 0.9299 (mm) REVERT: D 74 ASN cc_start: 0.9057 (p0) cc_final: 0.8705 (p0) REVERT: D 160 ASN cc_start: 0.8519 (m-40) cc_final: 0.8298 (m-40) REVERT: D 242 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8481 (tp40) REVERT: D 277 GLN cc_start: 0.8960 (pm20) cc_final: 0.8738 (pm20) REVERT: D 314 TYR cc_start: 0.8794 (m-80) cc_final: 0.8564 (m-80) REVERT: E 62 THR cc_start: 0.8786 (p) cc_final: 0.8495 (t) REVERT: E 124 THR cc_start: 0.9529 (m) cc_final: 0.9156 (p) REVERT: E 130 ASP cc_start: 0.8435 (t0) cc_final: 0.8009 (m-30) REVERT: E 212 ASP cc_start: 0.8672 (m-30) cc_final: 0.8443 (t0) REVERT: E 354 VAL cc_start: 0.9114 (t) cc_final: 0.8867 (p) REVERT: F 34 GLU cc_start: 0.7662 (tt0) cc_final: 0.7455 (tt0) REVERT: F 169 ARG cc_start: 0.8527 (mtp180) cc_final: 0.8249 (mtm180) REVERT: F 202 LEU cc_start: 0.8518 (tp) cc_final: 0.8258 (tt) REVERT: F 277 GLN cc_start: 0.9014 (pm20) cc_final: 0.8623 (pm20) REVERT: G 94 ASN cc_start: 0.8672 (p0) cc_final: 0.8355 (p0) REVERT: G 106 ASP cc_start: 0.7947 (p0) cc_final: 0.7408 (p0) REVERT: G 109 THR cc_start: 0.8991 (m) cc_final: 0.8417 (p) REVERT: H 87 ASP cc_start: 0.8359 (m-30) cc_final: 0.8136 (m-30) REVERT: H 184 ILE cc_start: 0.8887 (mm) cc_final: 0.8527 (mt) REVERT: H 269 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.7357 (mtm-85) REVERT: I 6 ILE cc_start: 0.9148 (mt) cc_final: 0.8615 (tp) REVERT: I 11 GLN cc_start: 0.8184 (tp40) cc_final: 0.7863 (tm-30) REVERT: I 24 THR cc_start: 0.8699 (t) cc_final: 0.8475 (t) REVERT: I 26 SER cc_start: 0.7718 (p) cc_final: 0.7429 (p) REVERT: I 43 THR cc_start: 0.9421 (p) cc_final: 0.8866 (t) REVERT: I 57 TYR cc_start: 0.9212 (p90) cc_final: 0.8752 (p90) REVERT: J 11 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7488 (tp40) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2927 time to fit residues: 162.0584 Evaluate side-chains 250 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 50.0000 chunk 32 optimal weight: 30.0000 chunk 166 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 45 GLN C 227 HIS D 94 ASN D 170 ASN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 348 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN H 96 GLN ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23187 Z= 0.252 Angle : 0.531 13.195 32030 Z= 0.283 Chirality : 0.039 0.250 3853 Planarity : 0.004 0.056 3906 Dihedral : 15.015 114.799 4592 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -0.10 (0.15), residues: 2930 helix: 1.88 (0.18), residues: 925 sheet: 0.56 (0.24), residues: 476 loop : -1.61 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 316 HIS 0.008 0.001 HIS G 227 PHE 0.020 0.002 PHE D 245 TYR 0.023 0.002 TYR H 344 ARG 0.004 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9578 (m-40) cc_final: 0.9376 (m110) REVERT: A 263 TRP cc_start: 0.9255 (m-10) cc_final: 0.9054 (m-10) REVERT: B 17 ILE cc_start: 0.8918 (mt) cc_final: 0.8571 (pt) REVERT: B 102 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7469 (mmm-85) REVERT: B 125 GLU cc_start: 0.7739 (tp30) cc_final: 0.7075 (tm-30) REVERT: C 58 TRP cc_start: 0.8955 (m-10) cc_final: 0.8527 (m-10) REVERT: C 168 TRP cc_start: 0.8376 (m100) cc_final: 0.8072 (m-10) REVERT: C 238 ILE cc_start: 0.9262 (mm) cc_final: 0.8944 (tt) REVERT: C 348 ASN cc_start: 0.9180 (t0) cc_final: 0.8383 (t0) REVERT: D 72 ILE cc_start: 0.9566 (mt) cc_final: 0.9325 (mm) REVERT: D 74 ASN cc_start: 0.9020 (p0) cc_final: 0.8693 (p0) REVERT: D 202 LEU cc_start: 0.8645 (tp) cc_final: 0.8247 (tt) REVERT: E 62 THR cc_start: 0.8789 (p) cc_final: 0.8491 (t) REVERT: E 124 THR cc_start: 0.9542 (m) cc_final: 0.9165 (p) REVERT: E 130 ASP cc_start: 0.8443 (t0) cc_final: 0.8079 (m-30) REVERT: E 287 ASP cc_start: 0.7766 (p0) cc_final: 0.7472 (p0) REVERT: E 354 VAL cc_start: 0.9110 (t) cc_final: 0.8865 (p) REVERT: F 64 ARG cc_start: 0.8348 (mtm110) cc_final: 0.8143 (mtm110) REVERT: F 189 VAL cc_start: 0.9635 (t) cc_final: 0.9354 (m) REVERT: F 202 LEU cc_start: 0.8606 (tp) cc_final: 0.8352 (tt) REVERT: F 277 GLN cc_start: 0.9020 (pm20) cc_final: 0.8641 (pm20) REVERT: G 94 ASN cc_start: 0.8762 (p0) cc_final: 0.8437 (p0) REVERT: G 106 ASP cc_start: 0.8029 (p0) cc_final: 0.7413 (p0) REVERT: H 87 ASP cc_start: 0.8424 (m-30) cc_final: 0.8135 (m-30) REVERT: H 184 ILE cc_start: 0.8898 (mm) cc_final: 0.8536 (mt) REVERT: H 269 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7360 (mtm-85) REVERT: H 302 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7316 (mm-30) REVERT: I 11 GLN cc_start: 0.8224 (tp40) cc_final: 0.7926 (tm-30) REVERT: I 24 THR cc_start: 0.8635 (t) cc_final: 0.8400 (t) REVERT: I 26 SER cc_start: 0.7731 (p) cc_final: 0.7482 (p) REVERT: I 43 THR cc_start: 0.9452 (p) cc_final: 0.8895 (t) REVERT: J 11 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7828 (tp40) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2966 time to fit residues: 156.8486 Evaluate side-chains 239 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 27 optimal weight: 40.0000 chunk 228 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS C 227 HIS D 94 ASN D 170 ASN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 348 ASN F 170 ASN F 348 ASN G 160 ASN G 227 HIS G 348 ASN H 96 GLN H 159 HIS ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23187 Z= 0.261 Angle : 0.533 10.838 32030 Z= 0.285 Chirality : 0.039 0.255 3853 Planarity : 0.004 0.053 3906 Dihedral : 14.994 114.729 4592 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.06 % Allowed : 0.86 % Favored : 99.08 % 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: -0.11 (0.15), residues: 2930 helix: 1.89 (0.18), residues: 925 sheet: 0.52 (0.24), residues: 476 loop : -1.62 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP B 316 HIS 0.006 0.001 HIS G 227 PHE 0.015 0.002 PHE F 166 TYR 0.021 0.002 TYR G 344 ARG 0.012 0.001 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8020 (ttp-170) REVERT: A 237 ASN cc_start: 0.9587 (m-40) cc_final: 0.9368 (m110) REVERT: B 17 ILE cc_start: 0.8928 (mt) cc_final: 0.8524 (pt) REVERT: B 102 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7317 (mtt90) REVERT: B 125 GLU cc_start: 0.7760 (tp30) cc_final: 0.7093 (tm-30) REVERT: C 58 TRP cc_start: 0.8972 (m-10) cc_final: 0.8548 (m-10) REVERT: C 168 TRP cc_start: 0.8346 (m100) cc_final: 0.8095 (m100) REVERT: C 238 ILE cc_start: 0.9275 (mm) cc_final: 0.8961 (tt) REVERT: C 334 ASP cc_start: 0.8800 (m-30) cc_final: 0.8439 (m-30) REVERT: C 348 ASN cc_start: 0.9139 (t0) cc_final: 0.8514 (t0) REVERT: D 72 ILE cc_start: 0.9559 (mt) cc_final: 0.9346 (mm) REVERT: D 74 ASN cc_start: 0.9077 (p0) cc_final: 0.8757 (p0) REVERT: D 91 GLN cc_start: 0.7992 (mm110) cc_final: 0.7461 (mm110) REVERT: E 62 THR cc_start: 0.8751 (p) cc_final: 0.8438 (t) REVERT: E 109 THR cc_start: 0.9248 (m) cc_final: 0.8553 (p) REVERT: E 124 THR cc_start: 0.9557 (m) cc_final: 0.9179 (p) REVERT: E 130 ASP cc_start: 0.8460 (t0) cc_final: 0.8102 (m-30) REVERT: E 287 ASP cc_start: 0.7728 (p0) cc_final: 0.7461 (p0) REVERT: E 354 VAL cc_start: 0.9109 (t) cc_final: 0.8861 (p) REVERT: F 189 VAL cc_start: 0.9636 (t) cc_final: 0.9373 (m) REVERT: F 202 LEU cc_start: 0.8616 (tp) cc_final: 0.8353 (tt) REVERT: F 277 GLN cc_start: 0.9040 (pm20) cc_final: 0.8656 (pm20) REVERT: G 94 ASN cc_start: 0.8774 (p0) cc_final: 0.8451 (p0) REVERT: G 106 ASP cc_start: 0.8022 (p0) cc_final: 0.7423 (p0) REVERT: G 193 TRP cc_start: 0.8729 (m-90) cc_final: 0.8428 (m-90) REVERT: H 87 ASP cc_start: 0.8462 (m-30) cc_final: 0.8151 (m-30) REVERT: H 184 ILE cc_start: 0.8905 (mm) cc_final: 0.8577 (mt) REVERT: H 269 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.7378 (mtm-85) REVERT: H 322 ASP cc_start: 0.7890 (t0) cc_final: 0.7610 (t0) REVERT: I 11 GLN cc_start: 0.8212 (tp40) cc_final: 0.7946 (tm-30) REVERT: I 24 THR cc_start: 0.8637 (t) cc_final: 0.8430 (t) REVERT: I 26 SER cc_start: 0.7701 (p) cc_final: 0.7474 (p) REVERT: I 43 THR cc_start: 0.9462 (p) cc_final: 0.8938 (t) REVERT: J 11 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7793 (tp40) outliers start: 1 outliers final: 1 residues processed: 317 average time/residue: 0.3132 time to fit residues: 162.4550 Evaluate side-chains 230 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 10.0000 chunk 278 optimal weight: 20.0000 chunk 254 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 HIS ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 227 HIS ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN J 12 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23187 Z= 0.413 Angle : 0.636 10.705 32030 Z= 0.341 Chirality : 0.042 0.288 3853 Planarity : 0.004 0.052 3906 Dihedral : 15.199 112.927 4592 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -0.43 (0.15), residues: 2930 helix: 1.51 (0.18), residues: 942 sheet: 0.35 (0.24), residues: 470 loop : -1.76 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP B 316 HIS 0.008 0.001 HIS G 275 PHE 0.023 0.002 PHE D 245 TYR 0.022 0.002 TYR H 344 ARG 0.018 0.001 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.512 Fit side-chains revert: symmetry clash REVERT: B 125 GLU cc_start: 0.7818 (tp30) cc_final: 0.7205 (tm-30) REVERT: C 58 TRP cc_start: 0.9029 (m-10) cc_final: 0.8444 (m-10) REVERT: C 168 TRP cc_start: 0.8437 (m100) cc_final: 0.8224 (m100) REVERT: C 238 ILE cc_start: 0.9302 (mm) cc_final: 0.9039 (tt) REVERT: C 348 ASN cc_start: 0.9147 (t0) cc_final: 0.8449 (t0) REVERT: D 72 ILE cc_start: 0.9571 (mt) cc_final: 0.9324 (mm) REVERT: D 91 GLN cc_start: 0.7932 (mm110) cc_final: 0.7410 (mm110) REVERT: D 242 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8511 (mm-40) REVERT: E 62 THR cc_start: 0.8751 (p) cc_final: 0.8506 (t) REVERT: E 124 THR cc_start: 0.9572 (m) cc_final: 0.9253 (p) REVERT: E 130 ASP cc_start: 0.8545 (t0) cc_final: 0.8228 (m-30) REVERT: E 287 ASP cc_start: 0.7736 (p0) cc_final: 0.7405 (p0) REVERT: E 354 VAL cc_start: 0.9163 (t) cc_final: 0.8863 (p) REVERT: F 109 THR cc_start: 0.9297 (m) cc_final: 0.8525 (p) REVERT: F 202 LEU cc_start: 0.8761 (tp) cc_final: 0.8495 (tt) REVERT: F 277 GLN cc_start: 0.9152 (pm20) cc_final: 0.8798 (pm20) REVERT: G 106 ASP cc_start: 0.8068 (p0) cc_final: 0.7461 (p0) REVERT: G 193 TRP cc_start: 0.9017 (m-90) cc_final: 0.8556 (m-10) REVERT: G 344 TYR cc_start: 0.9158 (t80) cc_final: 0.8913 (t80) REVERT: H 87 ASP cc_start: 0.8497 (m-30) cc_final: 0.8192 (m-30) REVERT: H 269 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.7571 (mtm-85) REVERT: I 6 ILE cc_start: 0.9140 (mt) cc_final: 0.8774 (tp) REVERT: I 11 GLN cc_start: 0.8390 (tp40) cc_final: 0.8002 (tp-100) REVERT: I 43 THR cc_start: 0.9509 (p) cc_final: 0.9029 (t) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2949 time to fit residues: 138.0129 Evaluate side-chains 210 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 0.5980 chunk 286 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 300 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 237 ASN B 42 HIS ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 196 HIS ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 GLN D 348 ASN E 348 ASN F 348 ASN G 348 ASN ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN I 53 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23187 Z= 0.142 Angle : 0.505 11.223 32030 Z= 0.263 Chirality : 0.038 0.231 3853 Planarity : 0.004 0.050 3906 Dihedral : 14.969 102.744 4592 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.04 (0.16), residues: 2930 helix: 2.10 (0.18), residues: 918 sheet: 0.42 (0.24), residues: 476 loop : -1.49 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 316 HIS 0.010 0.001 HIS G 227 PHE 0.016 0.001 PHE B 37 TYR 0.016 0.001 TYR G 290 ARG 0.010 0.000 ARG H 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.8471 (tpp80) cc_final: 0.7914 (ttp-170) REVERT: A 237 ASN cc_start: 0.9594 (m-40) cc_final: 0.9282 (m110) REVERT: B 17 ILE cc_start: 0.8888 (mt) cc_final: 0.8525 (pt) REVERT: B 125 GLU cc_start: 0.7379 (tp30) cc_final: 0.6875 (tm-30) REVERT: C 58 TRP cc_start: 0.8808 (m-10) cc_final: 0.8594 (m-10) REVERT: C 238 ILE cc_start: 0.9248 (mm) cc_final: 0.8957 (tt) REVERT: C 285 THR cc_start: 0.8299 (p) cc_final: 0.8096 (t) REVERT: C 348 ASN cc_start: 0.9135 (t0) cc_final: 0.8469 (t0) REVERT: D 72 ILE cc_start: 0.9586 (mt) cc_final: 0.9351 (mm) REVERT: D 74 ASN cc_start: 0.9054 (p0) cc_final: 0.8756 (p0) REVERT: D 91 GLN cc_start: 0.7890 (mm110) cc_final: 0.7508 (mm110) REVERT: D 242 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8417 (mm-40) REVERT: D 302 GLU cc_start: 0.8138 (tp30) cc_final: 0.7870 (tp30) REVERT: D 344 TYR cc_start: 0.9027 (t80) cc_final: 0.8791 (t80) REVERT: E 124 THR cc_start: 0.9558 (m) cc_final: 0.9203 (p) REVERT: E 130 ASP cc_start: 0.8399 (t0) cc_final: 0.8021 (m-30) REVERT: E 354 VAL cc_start: 0.9132 (t) cc_final: 0.8831 (p) REVERT: F 34 GLU cc_start: 0.7945 (tt0) cc_final: 0.7554 (tt0) REVERT: F 189 VAL cc_start: 0.9600 (t) cc_final: 0.9345 (m) REVERT: F 202 LEU cc_start: 0.8529 (tp) cc_final: 0.8287 (tt) REVERT: F 245 PHE cc_start: 0.8981 (m-80) cc_final: 0.8680 (m-10) REVERT: F 277 GLN cc_start: 0.8974 (pm20) cc_final: 0.8487 (pm20) REVERT: G 106 ASP cc_start: 0.7927 (p0) cc_final: 0.7302 (p0) REVERT: G 193 TRP cc_start: 0.8923 (m-90) cc_final: 0.8396 (m-10) REVERT: G 332 LEU cc_start: 0.9152 (mm) cc_final: 0.8846 (mt) REVERT: H 87 ASP cc_start: 0.8308 (m-30) cc_final: 0.8072 (m-30) REVERT: H 169 ARG cc_start: 0.8684 (mtp-110) cc_final: 0.8478 (mtp-110) REVERT: H 184 ILE cc_start: 0.8880 (mm) cc_final: 0.8541 (mt) REVERT: H 269 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.7476 (mtm-85) REVERT: H 302 GLU cc_start: 0.8293 (tt0) cc_final: 0.7743 (tt0) REVERT: I 11 GLN cc_start: 0.8141 (tp40) cc_final: 0.7866 (tm-30) REVERT: I 24 THR cc_start: 0.8580 (t) cc_final: 0.8315 (t) REVERT: I 43 THR cc_start: 0.9373 (p) cc_final: 0.8897 (t) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2921 time to fit residues: 163.5829 Evaluate side-chains 259 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 0.1980 chunk 255 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 35 optimal weight: 0.0050 chunk 66 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 overall best weight: 2.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 196 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 348 ASN F 348 ASN G 170 ASN G 348 ASN H 96 GLN ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN J 12 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117001 restraints weight = 38497.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119190 restraints weight = 24418.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120757 restraints weight = 17341.661| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23187 Z= 0.202 Angle : 0.516 10.629 32030 Z= 0.269 Chirality : 0.038 0.252 3853 Planarity : 0.004 0.058 3906 Dihedral : 14.914 95.997 4592 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.09 (0.16), residues: 2930 helix: 2.13 (0.18), residues: 917 sheet: 0.49 (0.24), residues: 478 loop : -1.46 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 228 HIS 0.012 0.001 HIS H 343 PHE 0.024 0.001 PHE F 33 TYR 0.019 0.002 TYR G 344 ARG 0.007 0.000 ARG G 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.17 seconds wall clock time: 80 minutes 49.40 seconds (4849.40 seconds total)