Starting phenix.real_space_refine on Mon Mar 18 12:36:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik3_35504/03_2024/8ik3_35504_updated.pdb" } resolution = 3.3 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= 0.015 sd= 0.069 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 16 5.49 5 S 104 5.16 5 C 13281 2.51 5 N 3731 2.21 5 O 3806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 231": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 231": "OD1" <-> "OD2" Residue "G GLU 316": "OE1" <-> "OE2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F ASP 231": "OD1" <-> "OD2" Residue "F ASP 301": "OD1" <-> "OD2" Residue "H TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H GLU 282": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20938 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2587 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2583 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Chain: "C" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2567 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2569 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2567 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2569 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2567 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2569 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1'A1SY B 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY B 601 " occ=0.50 residue: pdb=" C1'A1SY D 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY D 601 " occ=0.50 residue: pdb=" C1'A1SY G 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY G 601 " occ=0.50 residue: pdb=" C1'A1SY F 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY F 601 " occ=0.50 Time building chain proxies: 10.38, per 1000 atoms: 0.50 Number of scatterers: 20938 At special positions: 0 Unit cell: (89.01, 168.36, 113.16, 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 104 16.00 P 16 15.00 O 3806 8.00 N 3731 7.00 C 13281 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: 7.73 Conformation dependent library (CDL) restraints added in 4.0 seconds 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 24 sheets defined 52.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 40 through 71 removed outlier: 3.853A pdb=" N LEU A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 81 through 88 removed outlier: 3.900A pdb=" N VAL A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 108 removed outlier: 3.737A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 134 Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.711A pdb=" N SER A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 removed outlier: 4.780A pdb=" N ARG A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 4.130A pdb=" N GLN A 176 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A 185 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.784A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 301 removed outlier: 3.577A pdb=" N LYS A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'B' and resid 17 through 35 Processing helix chain 'B' and resid 40 through 69 removed outlier: 3.731A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 81 through 88 removed outlier: 3.551A pdb=" N VAL B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 118 through 134 removed outlier: 3.657A pdb=" N ALA B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 4.539A pdb=" N ARG B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 263 through 271 Processing helix chain 'B' and resid 283 through 300 removed outlier: 3.933A pdb=" N ALA B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 4.133A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 35 Processing helix chain 'C' and resid 40 through 69 removed outlier: 3.675A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 107 removed outlier: 3.932A pdb=" N PHE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N TYR C 107 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 134 Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.897A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 Processing helix chain 'C' and resid 168 through 171 No H-bonds generated for 'chain 'C' and resid 168 through 171' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 263 through 272 removed outlier: 3.684A pdb=" N SER C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 300 removed outlier: 3.740A pdb=" N CYS C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.830A pdb=" N HIS C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 35 Processing helix chain 'D' and resid 40 through 71 removed outlier: 3.522A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ARG D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.522A pdb=" N ALA D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 108 removed outlier: 3.501A pdb=" N SER D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 134 removed outlier: 3.759A pdb=" N LEU D 121 " --> pdb=" O PHE D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 150 removed outlier: 4.246A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 171 removed outlier: 4.677A pdb=" N ARG D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 removed outlier: 4.387A pdb=" N GLN D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 177 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 178 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG D 180 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 183 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 272 removed outlier: 3.703A pdb=" N SER D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 301 removed outlier: 3.988A pdb=" N ALA D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 Processing helix chain 'E' and resid 17 through 35 Processing helix chain 'E' and resid 40 through 72 removed outlier: 3.803A pdb=" N ALA E 67 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU E 68 " --> pdb=" O CYS E 64 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N HIS E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 92 through 107 removed outlier: 3.757A pdb=" N PHE E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 155 through 166 Processing helix chain 'E' and resid 168 through 185 Proline residue: E 173 - end of helix removed outlier: 4.690A pdb=" N GLN E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA E 177 " --> pdb=" O PRO E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 272 removed outlier: 3.695A pdb=" N SER E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 300 removed outlier: 3.738A pdb=" N CYS E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 325 through 334 Processing helix chain 'G' and resid 18 through 35 Processing helix chain 'G' and resid 40 through 76 removed outlier: 4.089A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 68 " --> pdb=" O CYS G 64 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ARG G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N HIS G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS G 74 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N SER G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 86 Processing helix chain 'G' and resid 94 through 108 Processing helix chain 'G' and resid 118 through 134 Processing helix chain 'G' and resid 141 through 150 removed outlier: 3.838A pdb=" N ALA G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 171 removed outlier: 4.533A pdb=" N ARG G 169 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU G 170 " --> pdb=" O GLY G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 185 removed outlier: 3.963A pdb=" N THR G 181 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN G 184 " --> pdb=" O ARG G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 271 Processing helix chain 'G' and resid 283 through 300 removed outlier: 3.617A pdb=" N CYS G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 334 Processing helix chain 'F' and resid 17 through 35 Processing helix chain 'F' and resid 40 through 72 removed outlier: 3.879A pdb=" N ALA F 67 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU F 68 " --> pdb=" O CYS F 64 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N HIS F 72 " --> pdb=" O GLU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 88 removed outlier: 4.092A pdb=" N VAL F 85 " --> pdb=" O TYR F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 107 removed outlier: 4.253A pdb=" N TYR F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 134 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 155 through 166 Processing helix chain 'F' and resid 168 through 171 No H-bonds generated for 'chain 'F' and resid 168 through 171' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 263 through 273 removed outlier: 3.992A pdb=" N GLN F 273 " --> pdb=" O PHE F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 301 removed outlier: 3.798A pdb=" N CYS F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP F 301 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 325 through 334 removed outlier: 3.502A pdb=" N HIS F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 35 Processing helix chain 'H' and resid 40 through 76 removed outlier: 3.816A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN H 61 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU H 68 " --> pdb=" O CYS H 64 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N HIS H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 88 removed outlier: 3.716A pdb=" N CYS H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 108 removed outlier: 3.508A pdb=" N SER H 108 " --> pdb=" O TYR H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 134 Processing helix chain 'H' and resid 141 through 150 removed outlier: 3.504A pdb=" N SER H 145 " --> pdb=" O PRO H 141 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA H 146 " --> pdb=" O ALA H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 171 removed outlier: 4.330A pdb=" N ARG H 169 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU H 170 " --> pdb=" O GLY H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 185 removed outlier: 3.806A pdb=" N THR H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 272 removed outlier: 3.586A pdb=" N SER H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 301 removed outlier: 3.691A pdb=" N ALA H 288 " --> pdb=" O ARG H 284 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 293 " --> pdb=" O LYS H 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP H 301 " --> pdb=" O ASP H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 334 Processing sheet with id= A, first strand: chain 'A' and resid 198 through 203 removed outlier: 3.879A pdb=" N ARG A 310 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 200 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 314 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 228 through 230 Processing sheet with id= C, first strand: chain 'A' and resid 219 through 224 removed outlier: 3.542A pdb=" N ARG A 220 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 247 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 198 through 203 removed outlier: 3.857A pdb=" N TYR B 314 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 228 through 230 Processing sheet with id= F, first strand: chain 'B' and resid 219 through 224 removed outlier: 7.058A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 257 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU B 249 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 198 through 203 removed outlier: 3.867A pdb=" N TYR C 314 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 228 through 230 Processing sheet with id= I, first strand: chain 'C' and resid 219 through 224 removed outlier: 3.609A pdb=" N ARG C 220 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 255 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU C 249 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 198 through 203 removed outlier: 3.646A pdb=" N TYR D 314 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 228 through 230 Processing sheet with id= L, first strand: chain 'D' and resid 220 through 224 removed outlier: 3.510A pdb=" N ARG D 220 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 255 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU D 249 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 198 through 203 removed outlier: 3.725A pdb=" N TYR E 314 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= O, first strand: chain 'E' and resid 219 through 224 removed outlier: 6.949A pdb=" N ILE E 244 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 257 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY E 255 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU E 249 " --> pdb=" O ARG E 253 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 198 through 203 Processing sheet with id= Q, first strand: chain 'G' and resid 228 through 230 Processing sheet with id= R, first strand: chain 'G' and resid 220 through 224 removed outlier: 3.544A pdb=" N ARG G 220 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE G 244 " --> pdb=" O LEU G 222 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY G 255 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU G 249 " --> pdb=" O ARG G 253 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 198 through 203 removed outlier: 3.549A pdb=" N TYR F 314 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 228 through 230 Processing sheet with id= U, first strand: chain 'F' and resid 219 through 224 removed outlier: 7.399A pdb=" N ILE F 244 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY F 255 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU F 249 " --> pdb=" O ARG F 253 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 198 through 203 removed outlier: 3.643A pdb=" N TYR H 314 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 228 through 230 Processing sheet with id= X, first strand: chain 'H' and resid 220 through 224 removed outlier: 6.803A pdb=" N ILE H 244 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY H 255 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU H 249 " --> pdb=" O ARG H 253 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 8.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3299 1.31 - 1.44: 5848 1.44 - 1.56: 12123 1.56 - 1.69: 3 1.69 - 1.81: 158 Bond restraints: 21431 Sorted by residual: bond pdb=" O28B1SY F 601 " pdb=" P27B1SY F 601 " ideal model delta sigma weight residual 1.636 1.751 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" O28A1SY F 601 " pdb=" P27A1SY F 601 " ideal model delta sigma weight residual 1.636 1.751 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" O28B1SY G 601 " pdb=" P27B1SY G 601 " ideal model delta sigma weight residual 1.636 1.750 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" O28A1SY G 601 " pdb=" P27A1SY G 601 " ideal model delta sigma weight residual 1.636 1.750 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" O28A1SY B 601 " pdb=" P27A1SY B 601 " ideal model delta sigma weight residual 1.636 1.748 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 21426 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.18: 460 105.18 - 112.38: 10909 112.38 - 119.59: 7269 119.59 - 126.79: 10195 126.79 - 133.99: 346 Bond angle restraints: 29179 Sorted by residual: angle pdb=" CA PRO C 217 " pdb=" N PRO C 217 " pdb=" CD PRO C 217 " ideal model delta sigma weight residual 112.00 106.04 5.96 1.40e+00 5.10e-01 1.81e+01 angle pdb=" N SER B 5 " pdb=" CA SER B 5 " pdb=" C SER B 5 " ideal model delta sigma weight residual 114.56 110.31 4.25 1.27e+00 6.20e-01 1.12e+01 angle pdb=" N VAL B 147 " pdb=" CA VAL B 147 " pdb=" C VAL B 147 " ideal model delta sigma weight residual 113.39 108.58 4.81 1.47e+00 4.63e-01 1.07e+01 angle pdb=" C LEU D 170 " pdb=" N ILE D 171 " pdb=" CA ILE D 171 " ideal model delta sigma weight residual 121.85 118.37 3.48 1.19e+00 7.06e-01 8.56e+00 angle pdb=" N SER E 5 " pdb=" CA SER E 5 " pdb=" C SER E 5 " ideal model delta sigma weight residual 114.56 110.97 3.59 1.27e+00 6.20e-01 8.01e+00 ... (remaining 29174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 12446 35.72 - 71.45: 260 71.45 - 107.17: 31 107.17 - 142.90: 8 142.90 - 178.62: 16 Dihedral angle restraints: 12761 sinusoidal: 5163 harmonic: 7598 Sorted by residual: dihedral pdb=" C16A1SY G 601 " pdb=" O17A1SY G 601 " pdb=" P18A1SY G 601 " pdb=" O20A1SY G 601 " ideal model delta sinusoidal sigma weight residual 266.83 88.21 178.62 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3'B1SY B 601 " pdb=" C16B1SY B 601 " pdb=" C4'B1SY B 601 " pdb=" O17B1SY B 601 " ideal model delta sinusoidal sigma weight residual 116.11 -61.93 178.04 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3'B1SY G 601 " pdb=" C16B1SY G 601 " pdb=" C4'B1SY G 601 " pdb=" O17B1SY G 601 " ideal model delta sinusoidal sigma weight residual 116.11 -66.31 -177.58 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2143 0.034 - 0.067: 858 0.067 - 0.101: 154 0.101 - 0.134: 109 0.134 - 0.168: 7 Chirality restraints: 3271 Sorted by residual: chirality pdb=" CG LEU D 44 " pdb=" CB LEU D 44 " pdb=" CD1 LEU D 44 " pdb=" CD2 LEU D 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA ARG B 284 " pdb=" N ARG B 284 " pdb=" C ARG B 284 " pdb=" CB ARG B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ASP B 301 " pdb=" N ASP B 301 " pdb=" C ASP B 301 " pdb=" CB ASP B 301 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 3268 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 216 " -0.085 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C 217 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 216 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO B 217 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 164 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C TYR D 164 " -0.026 2.00e-02 2.50e+03 pdb=" O TYR D 164 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 165 " 0.009 2.00e-02 2.50e+03 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 388 2.70 - 3.25: 19759 3.25 - 3.80: 30884 3.80 - 4.35: 38299 4.35 - 4.90: 66680 Nonbonded interactions: 156010 Sorted by model distance: nonbonded pdb=" OE1 GLU A 69 " pdb=" OH TYR A 77 " model vdw 2.148 2.440 nonbonded pdb=" OE1 GLU D 69 " pdb=" OH TYR D 77 " model vdw 2.150 2.440 nonbonded pdb=" O LEU C 98 " pdb=" OG SER C 102 " model vdw 2.163 2.440 nonbonded pdb=" O SER F 127 " pdb=" ND2 ASN F 131 " model vdw 2.178 2.520 nonbonded pdb=" O ALA A 302 " pdb=" OG SER A 305 " model vdw 2.180 2.440 ... (remaining 156005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) selection = (chain 'B' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 106 or (resid 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 335)) selection = (chain 'C' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 335)) selection = (chain 'D' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) selection = (chain 'E' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 335)) selection = (chain 'F' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 335)) selection = (chain 'G' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) selection = (chain 'H' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.010 Extract box with map and model: 6.240 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 54.310 Find NCS groups from input model: 1.790 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: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.006 0.115 21431 Z= 0.369 Angle : 0.629 7.835 29179 Z= 0.320 Chirality : 0.040 0.168 3271 Planarity : 0.005 0.126 3683 Dihedral : 17.657 178.625 7891 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.09 % Allowed : 0.32 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2579 helix: 1.88 (0.15), residues: 1361 sheet: 0.74 (0.55), residues: 106 loop : -1.00 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.006 0.001 HIS D 157 PHE 0.022 0.002 PHE C 279 TYR 0.017 0.001 TYR B 261 ARG 0.008 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 217 time to evaluate : 1.989 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8361 (t80) cc_final: 0.7930 (t80) REVERT: B 107 TYR cc_start: 0.7500 (t80) cc_final: 0.6871 (t80) REVERT: E 74 HIS cc_start: 0.6700 (t70) cc_final: 0.6382 (t70) REVERT: G 221 PHE cc_start: 0.6498 (t80) cc_final: 0.5806 (t80) REVERT: G 269 PHE cc_start: 0.6787 (t80) cc_final: 0.6448 (t80) REVERT: H 120 MET cc_start: 0.7847 (mmt) cc_final: 0.7543 (mmm) outliers start: 2 outliers final: 1 residues processed: 218 average time/residue: 0.3256 time to fit residues: 110.2168 Evaluate side-chains 150 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 HIS B 218 ASN G 42 HIS ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21431 Z= 0.220 Angle : 0.545 6.974 29179 Z= 0.267 Chirality : 0.039 0.215 3271 Planarity : 0.004 0.077 3683 Dihedral : 15.805 179.446 3042 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.82 % Allowed : 6.99 % Favored : 92.20 % 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: 1.01 (0.17), residues: 2579 helix: 1.87 (0.15), residues: 1375 sheet: 0.73 (0.52), residues: 110 loop : -0.92 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS E 332 PHE 0.016 0.002 PHE C 279 TYR 0.012 0.001 TYR F 186 ARG 0.003 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 2.529 Fit side-chains REVERT: B 107 TYR cc_start: 0.7471 (t80) cc_final: 0.6888 (t80) REVERT: C 100 LEU cc_start: 0.8417 (mm) cc_final: 0.8203 (mp) REVERT: D 185 HIS cc_start: 0.6473 (m90) cc_final: 0.6153 (t-90) REVERT: E 74 HIS cc_start: 0.6695 (t70) cc_final: 0.6423 (t70) REVERT: G 221 PHE cc_start: 0.5683 (t80) cc_final: 0.5369 (t80) REVERT: G 269 PHE cc_start: 0.6862 (t80) cc_final: 0.6540 (t80) REVERT: H 120 MET cc_start: 0.7852 (mmt) cc_final: 0.7548 (mmm) outliers start: 18 outliers final: 17 residues processed: 176 average time/residue: 0.3152 time to fit residues: 86.6480 Evaluate side-chains 168 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain H residue 205 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 40.0000 chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 251 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN G 42 HIS F 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21431 Z= 0.136 Angle : 0.478 9.011 29179 Z= 0.233 Chirality : 0.036 0.194 3271 Planarity : 0.004 0.063 3683 Dihedral : 15.460 177.631 3040 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.82 % Allowed : 10.21 % Favored : 88.97 % 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: 1.26 (0.18), residues: 2579 helix: 2.13 (0.15), residues: 1369 sheet: 0.63 (0.52), residues: 116 loop : -0.86 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 161 HIS 0.004 0.001 HIS G 332 PHE 0.013 0.001 PHE E 221 TYR 0.011 0.001 TYR F 186 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 2.465 Fit side-chains REVERT: B 107 TYR cc_start: 0.7457 (t80) cc_final: 0.6886 (t80) REVERT: D 116 PRO cc_start: 0.8177 (Cg_exo) cc_final: 0.7962 (Cg_endo) REVERT: D 301 ASP cc_start: 0.7751 (t0) cc_final: 0.7550 (t0) REVERT: E 74 HIS cc_start: 0.6629 (t70) cc_final: 0.6391 (t70) REVERT: E 287 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.6719 (mp10) REVERT: G 221 PHE cc_start: 0.5627 (t80) cc_final: 0.5170 (t80) REVERT: G 269 PHE cc_start: 0.6788 (t80) cc_final: 0.6496 (t80) REVERT: H 120 MET cc_start: 0.7832 (mmt) cc_final: 0.7524 (mmm) outliers start: 18 outliers final: 11 residues processed: 179 average time/residue: 0.3228 time to fit residues: 90.6747 Evaluate side-chains 161 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 40.0000 chunk 247 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 221 optimal weight: 0.0770 chunk 66 optimal weight: 8.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS F 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21431 Z= 0.302 Angle : 0.563 7.638 29179 Z= 0.273 Chirality : 0.040 0.199 3271 Planarity : 0.004 0.060 3683 Dihedral : 15.745 178.436 3040 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.81 % Allowed : 11.80 % Favored : 86.39 % 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: 1.04 (0.17), residues: 2579 helix: 1.97 (0.15), residues: 1362 sheet: 0.54 (0.52), residues: 110 loop : -0.97 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 161 HIS 0.007 0.001 HIS E 332 PHE 0.019 0.002 PHE C 279 TYR 0.013 0.001 TYR B 106 ARG 0.009 0.000 ARG C 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 2.212 Fit side-chains REVERT: A 301 ASP cc_start: 0.7609 (t0) cc_final: 0.7281 (t0) REVERT: B 107 TYR cc_start: 0.7476 (t80) cc_final: 0.6922 (t80) REVERT: B 211 ASN cc_start: 0.8223 (t0) cc_final: 0.7958 (t0) REVERT: B 225 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8257 (mp) REVERT: D 185 HIS cc_start: 0.6730 (m-70) cc_final: 0.6248 (t-90) REVERT: D 301 ASP cc_start: 0.7831 (t0) cc_final: 0.7609 (t0) REVERT: E 287 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.6792 (mp10) REVERT: G 221 PHE cc_start: 0.5668 (t80) cc_final: 0.5446 (t80) REVERT: G 269 PHE cc_start: 0.6799 (t80) cc_final: 0.6487 (t80) REVERT: F 222 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7668 (mt) REVERT: H 120 MET cc_start: 0.7868 (mmt) cc_final: 0.7560 (mmm) outliers start: 40 outliers final: 27 residues processed: 189 average time/residue: 0.3284 time to fit residues: 96.7024 Evaluate side-chains 184 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 50.0000 chunk 102 optimal weight: 5.9990 chunk 211 optimal weight: 50.0000 chunk 171 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 176 GLN E 176 GLN G 42 HIS F 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21431 Z= 0.205 Angle : 0.505 7.764 29179 Z= 0.246 Chirality : 0.037 0.214 3271 Planarity : 0.004 0.054 3683 Dihedral : 15.633 176.666 3040 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.68 % Allowed : 12.43 % Favored : 85.89 % 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: 1.13 (0.18), residues: 2579 helix: 2.06 (0.15), residues: 1362 sheet: 0.51 (0.53), residues: 110 loop : -0.94 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.005 0.001 HIS D 157 PHE 0.013 0.001 PHE C 291 TYR 0.016 0.001 TYR G 167 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 2.573 Fit side-chains REVERT: A 301 ASP cc_start: 0.7533 (t0) cc_final: 0.7238 (t0) REVERT: B 107 TYR cc_start: 0.7507 (t80) cc_final: 0.6962 (t80) REVERT: B 211 ASN cc_start: 0.8224 (t0) cc_final: 0.7928 (t0) REVERT: D 107 TYR cc_start: 0.8220 (t80) cc_final: 0.7940 (t80) REVERT: D 185 HIS cc_start: 0.6766 (m-70) cc_final: 0.6242 (t-90) REVERT: E 287 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.6768 (mp10) REVERT: G 224 LYS cc_start: 0.5750 (mmtm) cc_final: 0.5196 (mtpt) REVERT: G 269 PHE cc_start: 0.6781 (t80) cc_final: 0.6459 (t80) REVERT: F 222 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7668 (mt) REVERT: H 120 MET cc_start: 0.7878 (mmt) cc_final: 0.7563 (mmm) outliers start: 37 outliers final: 23 residues processed: 182 average time/residue: 0.3215 time to fit residues: 91.9460 Evaluate side-chains 173 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 7.9990 chunk 222 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 247 optimal weight: 30.0000 chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 20 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN D 242 ASN E 176 GLN G 42 HIS G 228 GLN F 252 GLN H 308 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21431 Z= 0.297 Angle : 0.559 7.976 29179 Z= 0.272 Chirality : 0.039 0.222 3271 Planarity : 0.004 0.053 3683 Dihedral : 15.793 176.622 3040 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.00 % Allowed : 13.38 % Favored : 84.62 % 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: 0.98 (0.17), residues: 2579 helix: 1.94 (0.15), residues: 1355 sheet: 0.44 (0.53), residues: 110 loop : -1.00 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 161 HIS 0.006 0.001 HIS D 157 PHE 0.016 0.002 PHE C 279 TYR 0.015 0.001 TYR A 107 ARG 0.005 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 2.432 Fit side-chains REVERT: A 196 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7326 (mm-40) REVERT: A 301 ASP cc_start: 0.7591 (t0) cc_final: 0.7315 (t0) REVERT: B 107 TYR cc_start: 0.7571 (t80) cc_final: 0.7035 (t80) REVERT: B 211 ASN cc_start: 0.8218 (t0) cc_final: 0.7918 (t0) REVERT: B 225 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 290 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8481 (tt) REVERT: D 107 TYR cc_start: 0.8240 (t80) cc_final: 0.7977 (t80) REVERT: D 185 HIS cc_start: 0.6850 (m-70) cc_final: 0.6293 (t-90) REVERT: E 225 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6055 (mt) REVERT: E 287 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: G 269 PHE cc_start: 0.6755 (t80) cc_final: 0.6410 (t80) REVERT: F 222 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7617 (mt) REVERT: H 120 MET cc_start: 0.7901 (mmt) cc_final: 0.7614 (mmm) outliers start: 44 outliers final: 28 residues processed: 186 average time/residue: 0.3136 time to fit residues: 91.6656 Evaluate side-chains 182 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 246 optimal weight: 0.0970 chunk 154 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN E 176 GLN G 42 HIS F 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21431 Z= 0.253 Angle : 0.530 8.010 29179 Z= 0.259 Chirality : 0.038 0.224 3271 Planarity : 0.004 0.049 3683 Dihedral : 15.755 175.323 3040 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.04 % Allowed : 13.61 % Favored : 84.35 % 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: 1.02 (0.18), residues: 2579 helix: 1.96 (0.15), residues: 1361 sheet: 0.42 (0.53), residues: 110 loop : -0.97 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 161 HIS 0.005 0.001 HIS E 332 PHE 0.013 0.001 PHE D 291 TYR 0.014 0.001 TYR G 167 ARG 0.003 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 2.306 Fit side-chains revert: symmetry clash REVERT: A 301 ASP cc_start: 0.7556 (t0) cc_final: 0.7337 (t0) REVERT: B 107 TYR cc_start: 0.7559 (t80) cc_final: 0.7044 (t80) REVERT: B 211 ASN cc_start: 0.8221 (t0) cc_final: 0.7902 (t0) REVERT: B 225 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 290 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8460 (tt) REVERT: D 107 TYR cc_start: 0.8230 (t80) cc_final: 0.7992 (t80) REVERT: D 185 HIS cc_start: 0.6896 (m-70) cc_final: 0.6313 (t-90) REVERT: E 225 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.5928 (mt) REVERT: E 287 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.6785 (mp10) REVERT: E 332 HIS cc_start: 0.7785 (t-90) cc_final: 0.7406 (m90) REVERT: G 269 PHE cc_start: 0.6741 (t80) cc_final: 0.6397 (t80) REVERT: G 308 ASN cc_start: 0.7914 (m-40) cc_final: 0.6614 (t0) REVERT: F 222 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7615 (mt) outliers start: 45 outliers final: 32 residues processed: 188 average time/residue: 0.3166 time to fit residues: 93.6437 Evaluate side-chains 188 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 335 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 193 optimal weight: 30.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN H 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21431 Z= 0.127 Angle : 0.464 8.781 29179 Z= 0.227 Chirality : 0.036 0.240 3271 Planarity : 0.004 0.050 3683 Dihedral : 15.354 172.900 3040 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.32 % Allowed : 14.56 % Favored : 84.12 % 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: 1.29 (0.18), residues: 2579 helix: 2.22 (0.15), residues: 1361 sheet: 0.74 (0.59), residues: 94 loop : -0.91 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 161 HIS 0.004 0.001 HIS G 332 PHE 0.013 0.001 PHE C 291 TYR 0.016 0.001 TYR G 167 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 2.429 Fit side-chains revert: symmetry clash REVERT: B 107 TYR cc_start: 0.7504 (t80) cc_final: 0.6978 (t80) REVERT: B 211 ASN cc_start: 0.8227 (t0) cc_final: 0.7894 (t0) REVERT: B 225 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8315 (mp) REVERT: D 107 TYR cc_start: 0.8188 (t80) cc_final: 0.7975 (t80) REVERT: D 185 HIS cc_start: 0.6735 (m-70) cc_final: 0.6224 (t-90) REVERT: E 225 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.5816 (mt) REVERT: E 287 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.6705 (mp10) REVERT: E 332 HIS cc_start: 0.7773 (t-90) cc_final: 0.7472 (m90) REVERT: G 269 PHE cc_start: 0.6694 (t80) cc_final: 0.6399 (t80) REVERT: G 308 ASN cc_start: 0.7831 (m-40) cc_final: 0.6580 (t0) REVERT: F 222 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7630 (mt) REVERT: F 224 LYS cc_start: 0.5853 (mmtm) cc_final: 0.5544 (mtpt) outliers start: 29 outliers final: 23 residues processed: 182 average time/residue: 0.3137 time to fit residues: 89.9300 Evaluate side-chains 181 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 335 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 215 optimal weight: 40.0000 chunk 229 optimal weight: 7.9990 chunk 138 optimal weight: 40.0000 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 217 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21431 Z= 0.260 Angle : 0.535 8.145 29179 Z= 0.259 Chirality : 0.038 0.226 3271 Planarity : 0.004 0.051 3683 Dihedral : 15.561 174.363 3040 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.59 % Allowed : 14.75 % Favored : 83.67 % 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: 1.15 (0.18), residues: 2579 helix: 2.10 (0.15), residues: 1356 sheet: 0.67 (0.58), residues: 94 loop : -0.95 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 161 HIS 0.005 0.001 HIS D 157 PHE 0.014 0.001 PHE D 291 TYR 0.015 0.001 TYR A 107 ARG 0.004 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 2.488 Fit side-chains revert: symmetry clash REVERT: B 107 TYR cc_start: 0.7564 (t80) cc_final: 0.7040 (t80) REVERT: B 211 ASN cc_start: 0.8220 (t0) cc_final: 0.7908 (t0) REVERT: B 225 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8331 (mp) REVERT: B 290 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8464 (tt) REVERT: D 107 TYR cc_start: 0.8196 (t80) cc_final: 0.7984 (t80) REVERT: D 185 HIS cc_start: 0.6852 (m-70) cc_final: 0.6303 (t-90) REVERT: E 225 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.5890 (mt) REVERT: E 287 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.6799 (mp10) REVERT: E 332 HIS cc_start: 0.7735 (t-90) cc_final: 0.7459 (m90) REVERT: G 269 PHE cc_start: 0.6728 (t80) cc_final: 0.6427 (t80) REVERT: G 308 ASN cc_start: 0.7851 (m-40) cc_final: 0.6641 (t0) REVERT: F 222 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7628 (mt) outliers start: 35 outliers final: 28 residues processed: 182 average time/residue: 0.3281 time to fit residues: 93.7164 Evaluate side-chains 186 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 335 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 234 optimal weight: 40.0000 chunk 203 optimal weight: 30.0000 chunk 21 optimal weight: 0.3980 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21431 Z= 0.188 Angle : 0.497 8.120 29179 Z= 0.242 Chirality : 0.037 0.232 3271 Planarity : 0.004 0.050 3683 Dihedral : 15.492 172.982 3040 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.45 % Allowed : 15.02 % Favored : 83.53 % 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: 1.21 (0.18), residues: 2579 helix: 2.16 (0.15), residues: 1356 sheet: 0.70 (0.58), residues: 94 loop : -0.94 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 161 HIS 0.005 0.001 HIS G 332 PHE 0.013 0.001 PHE C 291 TYR 0.014 0.001 TYR G 167 ARG 0.006 0.000 ARG B 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 2.373 Fit side-chains revert: symmetry clash REVERT: B 107 TYR cc_start: 0.7570 (t80) cc_final: 0.7066 (t80) REVERT: B 211 ASN cc_start: 0.8221 (t0) cc_final: 0.7912 (t0) REVERT: B 225 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 290 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8437 (tt) REVERT: D 107 TYR cc_start: 0.8188 (t80) cc_final: 0.7975 (t80) REVERT: D 185 HIS cc_start: 0.6775 (m-70) cc_final: 0.6264 (t-90) REVERT: E 225 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.5867 (mt) REVERT: E 287 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: E 332 HIS cc_start: 0.7647 (t-90) cc_final: 0.7433 (m90) REVERT: G 308 ASN cc_start: 0.7834 (m-40) cc_final: 0.6668 (t0) REVERT: F 222 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7596 (mt) REVERT: F 224 LYS cc_start: 0.5850 (mmtm) cc_final: 0.5501 (mtpt) REVERT: H 120 MET cc_start: 0.7880 (mmt) cc_final: 0.7592 (mmm) outliers start: 32 outliers final: 27 residues processed: 175 average time/residue: 0.3256 time to fit residues: 89.6285 Evaluate side-chains 181 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 335 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 203 optimal weight: 20.0000 chunk 85 optimal weight: 0.1980 chunk 208 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 178 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN C 176 GLN ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.196948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142980 restraints weight = 30514.434| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 5.59 r_work: 0.3152 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21431 Z= 0.130 Angle : 0.466 7.984 29179 Z= 0.228 Chirality : 0.036 0.235 3271 Planarity : 0.004 0.050 3683 Dihedral : 15.191 171.363 3040 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.23 % Allowed : 15.34 % Favored : 83.44 % 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: 1.37 (0.18), residues: 2579 helix: 2.30 (0.15), residues: 1354 sheet: 0.75 (0.58), residues: 94 loop : -0.86 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.004 0.000 HIS G 332 PHE 0.013 0.001 PHE C 291 TYR 0.015 0.001 TYR G 167 ARG 0.003 0.000 ARG A 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.46 seconds wall clock time: 68 minutes 30.92 seconds (4110.92 seconds total)