Starting phenix.real_space_refine (version: dev) on Tue Apr 5 03:24:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u68_20662/04_2022/6u68_20662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u68_20662/04_2022/6u68_20662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u68_20662/04_2022/6u68_20662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u68_20662/04_2022/6u68_20662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u68_20662/04_2022/6u68_20662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u68_20662/04_2022/6u68_20662.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10489 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 1561 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 265} Link IDs: {'PTRANS': 10, 'TRANS': 308} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 960 Unresolved non-hydrogen angles: 1243 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 19, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 29, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 504 Conformer: "B" Number of residues, atoms: 319, 1561 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 265} Link IDs: {'PTRANS': 10, 'TRANS': 308} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 960 Unresolved non-hydrogen angles: 1243 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 19, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 29, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 504 bond proxies already assigned to first conformer: 1557 Chain: "B" Number of atoms: 1566 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 1564 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 11, 'TRANS': 306} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 960 Unresolved non-hydrogen angles: 1240 Unresolved non-hydrogen dihedrals: 773 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 11, 'GLU:plan': 29, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 503 Conformer: "B" Number of residues, atoms: 318, 1564 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 11, 'TRANS': 306} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 960 Unresolved non-hydrogen angles: 1240 Unresolved non-hydrogen dihedrals: 773 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 11, 'GLU:plan': 29, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 503 bond proxies already assigned to first conformer: 1559 Chain: "C" Number of atoms: 1496 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 Conformer: "B" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 bond proxies already assigned to first conformer: 1489 Chain: "D" Number of atoms: 1496 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 Conformer: "B" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 bond proxies already assigned to first conformer: 1489 Chain: "E" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Chain: "F" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Chain: "G" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Time building chain proxies: 10.36, per 1000 atoms: 0.99 Number of scatterers: 10489 At special positions: 0 Unit cell: (138.096, 135.904, 121.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2133 8.00 N 2133 7.00 C 6223 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: 4.36 Conformation dependent library (CDL) restraints added in 3.5 seconds 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 16 sheets defined 47.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 19 through 43 removed outlier: 3.523A pdb=" N ILE A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 69 through 108 Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.893A pdb=" N GLU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.680A pdb=" N LEU A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 187 through 202 removed outlier: 4.066A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.522A pdb=" N MET A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.773A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.698A pdb=" N ASP A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.518A pdb=" N ASP A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.960A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 13 through 16 Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 69 through 99 removed outlier: 4.248A pdb=" N GLY B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.577A pdb=" N VAL B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 155' Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.748A pdb=" N GLY B 197 " --> pdb=" O HIS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.554A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.544A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.685A pdb=" N GLN B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.764A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 42 Processing helix chain 'C' and resid 45 through 58 Processing helix chain 'C' and resid 69 through 99 removed outlier: 4.050A pdb=" N GLY C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 131 removed outlier: 3.893A pdb=" N GLU C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.679A pdb=" N LEU C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 187 through 202 removed outlier: 4.066A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.522A pdb=" N MET C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.773A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.697A pdb=" N ASP C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.517A pdb=" N ASP C 284 " --> pdb=" O VAL C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.960A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 41 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 69 through 99 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.578A pdb=" N VAL D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 155' Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.747A pdb=" N GLY D 197 " --> pdb=" O HIS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.554A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 removed outlier: 3.545A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.684A pdb=" N GLN D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.765A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 removed outlier: 3.621A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.797A pdb=" N ILE E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 197 " --> pdb=" O HIS E 193 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.519A pdb=" N MET E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.894A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.636A pdb=" N VAL E 252 " --> pdb=" O GLU E 248 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP E 254 " --> pdb=" O MET E 250 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.567A pdb=" N ASP E 284 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 323 through 334 removed outlier: 3.572A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 removed outlier: 3.527A pdb=" N GLU F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 removed outlier: 3.884A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.889A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.736A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.630A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.613A pdb=" N MET F 250 " --> pdb=" O GLY F 246 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 252 " --> pdb=" O GLU F 248 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.813A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.550A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.811A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 3.621A pdb=" N GLU G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 154 Processing helix chain 'G' and resid 166 through 171 Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.797A pdb=" N ILE G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY G 197 " --> pdb=" O HIS G 193 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.519A pdb=" N MET G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.894A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.636A pdb=" N VAL G 252 " --> pdb=" O GLU G 248 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP G 254 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.567A pdb=" N ASP G 284 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.573A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 129 removed outlier: 3.526A pdb=" N GLU H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 155 removed outlier: 3.885A pdb=" N SER H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.889A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.736A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.631A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 256 removed outlier: 3.613A pdb=" N MET H 250 " --> pdb=" O GLY H 246 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL H 252 " --> pdb=" O GLU H 248 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.814A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.550A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.810A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR H 333 " --> pdb=" O ARG H 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.370A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 181 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLU A 210 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 183 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 209 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.582A pdb=" N GLY A 322 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 301 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.380A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 119 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.557A pdb=" N ARG B 263 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.371A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 181 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLU C 210 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 183 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 268 removed outlier: 3.582A pdb=" N GLY C 322 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.380A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA D 209 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.557A pdb=" N ARG D 263 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.652A pdb=" N VAL E 139 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL E 160 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL E 141 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 263 through 268 removed outlier: 3.859A pdb=" N GLY E 322 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 295 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU E 301 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.552A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N HIS F 117 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ILE F 182 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F 119 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE F 208 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU F 210 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL F 183 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 263 through 267 removed outlier: 6.648A pdb=" N ILE F 317 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL F 296 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.652A pdb=" N VAL G 139 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL G 141 " --> pdb=" O VAL G 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 263 through 268 removed outlier: 3.859A pdb=" N GLY G 322 " --> pdb=" O ARG G 263 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY G 295 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 301 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.553A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS H 117 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ILE H 182 " --> pdb=" O HIS H 117 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL H 119 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE H 208 " --> pdb=" O ARG H 179 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU H 210 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL H 183 " --> pdb=" O GLU H 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 267 removed outlier: 6.649A pdb=" N ILE H 317 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL H 296 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU H 319 " --> pdb=" O ILE H 294 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1929 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: 3.73 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 2133 1.28 - 1.35: 2114 1.35 - 1.42: 12 1.42 - 1.50: 2160 1.50 - 1.57: 4063 Bond restraints: 10482 Sorted by residual: bond pdb=" C VAL B 4 " pdb=" N ILE B 5 " ideal model delta sigma weight residual 1.335 1.294 0.041 1.21e-02 6.83e+03 1.15e+01 bond pdb=" N TRP B 52 " pdb=" CA TRP B 52 " ideal model delta sigma weight residual 1.459 1.420 0.040 1.21e-02 6.83e+03 1.07e+01 bond pdb=" N THR B 76 " pdb=" CA THR B 76 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.23e-02 6.61e+03 9.65e+00 bond pdb=" CA SER A 66 " pdb=" CB SER A 66 " ideal model delta sigma weight residual 1.537 1.492 0.046 1.47e-02 4.63e+03 9.59e+00 bond pdb=" N PHE A 75 " pdb=" CA PHE A 75 " ideal model delta sigma weight residual 1.459 1.422 0.037 1.19e-02 7.06e+03 9.57e+00 ... (remaining 10477 not shown) Histogram of bond angle deviations from ideal: 101.93 - 107.38: 163 107.38 - 112.84: 5397 112.84 - 118.29: 2289 118.29 - 123.74: 6588 123.74 - 129.19: 117 Bond angle restraints: 14554 Sorted by residual: angle pdb=" N VAL A 112 " pdb=" CA VAL A 112 " pdb=" C VAL A 112 " ideal model delta sigma weight residual 109.34 123.18 -13.84 2.08e+00 2.31e-01 4.43e+01 angle pdb=" C VAL B 18 " pdb=" N PRO B 19 " pdb=" CA PRO B 19 " ideal model delta sigma weight residual 119.78 126.44 -6.66 1.03e+00 9.43e-01 4.18e+01 angle pdb=" N ILE B 7 " pdb=" CA ILE B 7 " pdb=" C ILE B 7 " ideal model delta sigma weight residual 111.00 104.32 6.68 1.09e+00 8.42e-01 3.76e+01 angle pdb=" N ASP B 64 " pdb=" CA ASP B 64 " pdb=" C ASP B 64 " ideal model delta sigma weight residual 112.23 104.88 7.35 1.26e+00 6.30e-01 3.40e+01 angle pdb=" C VAL C 18 " pdb=" N PRO C 19 " pdb=" CA PRO C 19 " ideal model delta sigma weight residual 119.78 125.76 -5.98 1.03e+00 9.43e-01 3.37e+01 ... (remaining 14549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.35: 5610 5.35 - 10.70: 388 10.70 - 16.05: 32 16.05 - 21.41: 4 21.41 - 26.76: 2 Dihedral angle restraints: 6036 sinusoidal: 0 harmonic: 6036 Sorted by residual: dihedral pdb=" CA ASP G 145 " pdb=" C ASP G 145 " pdb=" N GLU G 146 " pdb=" CA GLU G 146 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ASP E 145 " pdb=" C ASP E 145 " pdb=" N GLU E 146 " pdb=" CA GLU E 146 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA GLU E 144 " pdb=" C GLU E 144 " pdb=" N ASP E 145 " pdb=" CA ASP E 145 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1378 0.059 - 0.117: 466 0.117 - 0.176: 99 0.176 - 0.234: 6 0.234 - 0.293: 4 Chirality restraints: 1953 Sorted by residual: chirality pdb=" CA THR B 59 " pdb=" N THR B 59 " pdb=" C THR B 59 " pdb=" CB THR B 59 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE B 5 " pdb=" N ILE B 5 " pdb=" C ILE B 5 " pdb=" CB ILE B 5 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA TYR C 62 " pdb=" N TYR C 62 " pdb=" C TYR C 62 " pdb=" CB TYR C 62 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1950 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 70 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C PRO D 70 " -0.050 2.00e-02 2.50e+03 pdb=" O PRO D 70 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU D 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C PRO B 70 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO B 70 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 71 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 60 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C VAL D 60 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL D 60 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY D 61 " 0.015 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 4545 2.91 - 3.41: 9221 3.41 - 3.91: 13945 3.91 - 4.40: 14477 4.40 - 4.90: 24789 Nonbonded interactions: 66977 Sorted by model distance: nonbonded pdb=" N SER D 66 " pdb=" O SER D 66 " model vdw 2.419 2.496 nonbonded pdb=" O ARG A 116 " pdb=" O HIS A 117 " model vdw 2.424 3.040 nonbonded pdb=" N SER B 66 " pdb=" O SER B 66 " model vdw 2.485 2.496 nonbonded pdb=" N ASP B 64 " pdb=" N TYR B 65 " model vdw 2.486 2.560 nonbonded pdb=" N PRO B 13 " pdb=" N ARG B 14 " model vdw 2.506 2.560 ... (remaining 66972 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 18 through 99 or resid 115 through 240 or resid 242 throug \ h 336)) selection = (chain 'B' and (resid 18 through 99 or (resid 115 and (name N or name CA or name \ C or name O )) or resid 116 through 240 or resid 242 through 336)) selection = (chain 'C' and (resid 18 through 99 or (resid 115 and (name N or name CA or name \ C or name O )) or resid 116 through 240 or resid 242 through 336)) selection = (chain 'D' and (resid 18 through 99 or (resid 115 and (name N or name CA or name \ C or name O )) or resid 116 through 240 or resid 242 through 336)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6223 2.51 5 N 2133 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 3.730 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 38.100 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 0.046 10482 Z= 0.420 Angle : 0.895 13.840 14554 Z= 0.643 Chirality : 0.062 0.293 1953 Planarity : 0.005 0.029 2126 Dihedral : 4.272 26.758 2130 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer Outliers : 0.00 % 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: -3.82 (0.15), residues: 2115 helix: -3.12 (0.12), residues: 1016 sheet: -0.25 (0.26), residues: 334 loop : -2.48 (0.17), residues: 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.191 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0969 time to fit residues: 8.5452 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 10482 Z= 0.400 Angle : 0.863 7.072 14554 Z= 0.547 Chirality : 0.055 0.138 1953 Planarity : 0.006 0.023 2126 Dihedral : 5.982 25.756 2130 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % 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: -2.06 (0.17), residues: 2115 helix: -1.63 (0.14), residues: 971 sheet: 0.28 (0.31), residues: 260 loop : -1.38 (0.20), residues: 884 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0966 time to fit residues: 8.7906 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 5.9990 chunk 59 optimal weight: 0.0050 chunk 158 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 0.0170 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 10482 Z= 0.182 Angle : 0.454 4.469 14554 Z= 0.288 Chirality : 0.050 0.134 1953 Planarity : 0.003 0.015 2126 Dihedral : 4.257 20.204 2130 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.00 % 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: -0.75 (0.18), residues: 2115 helix: -0.26 (0.16), residues: 997 sheet: 0.94 (0.35), residues: 216 loop : -1.02 (0.21), residues: 902 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1099 time to fit residues: 9.6910 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 20.0000 chunk 143 optimal weight: 0.2980 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 10482 Z= 0.201 Angle : 0.479 4.083 14554 Z= 0.307 Chirality : 0.050 0.135 1953 Planarity : 0.003 0.016 2126 Dihedral : 4.426 20.939 2130 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2115 helix: 0.13 (0.16), residues: 990 sheet: 0.86 (0.35), residues: 215 loop : -0.94 (0.21), residues: 910 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0944 time to fit residues: 8.4488 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 182 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.009 10482 Z= 0.087 Angle : 0.337 3.479 14554 Z= 0.212 Chirality : 0.049 0.134 1953 Planarity : 0.001 0.012 2126 Dihedral : 3.452 20.365 2130 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2115 helix: 0.99 (0.17), residues: 995 sheet: 0.96 (0.35), residues: 222 loop : -0.65 (0.22), residues: 898 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0980 time to fit residues: 8.7587 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 168 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.016 10482 Z= 0.204 Angle : 0.463 3.656 14554 Z= 0.295 Chirality : 0.051 0.136 1953 Planarity : 0.002 0.016 2126 Dihedral : 4.268 21.692 2130 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.00 % 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: 0.01 (0.19), residues: 2115 helix: 0.59 (0.17), residues: 976 sheet: 0.76 (0.35), residues: 217 loop : -0.76 (0.21), residues: 922 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0973 time to fit residues: 8.9416 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 8.9990 chunk 22 optimal weight: 0.0170 chunk 115 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 171 optimal weight: 0.1980 chunk 113 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 4.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 10482 Z= 0.191 Angle : 0.447 3.991 14554 Z= 0.285 Chirality : 0.050 0.134 1953 Planarity : 0.002 0.017 2126 Dihedral : 4.312 22.737 2130 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.00 % 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: -0.02 (0.19), residues: 2115 helix: 0.64 (0.17), residues: 952 sheet: 0.28 (0.35), residues: 223 loop : -0.68 (0.21), residues: 940 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.243 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0998 time to fit residues: 8.8613 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 40.0000 chunk 60 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 159 optimal weight: 40.0000 chunk 184 optimal weight: 6.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.8043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.029 10482 Z= 0.407 Angle : 0.710 6.425 14554 Z= 0.455 Chirality : 0.054 0.144 1953 Planarity : 0.004 0.022 2126 Dihedral : 5.885 30.026 2130 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.62 % Favored : 90.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.66 (0.17), residues: 2115 helix: -0.87 (0.15), residues: 939 sheet: -0.25 (0.35), residues: 224 loop : -1.46 (0.20), residues: 952 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0989 time to fit residues: 8.9069 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.8042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 10482 Z= 0.238 Angle : 0.509 4.945 14554 Z= 0.324 Chirality : 0.051 0.136 1953 Planarity : 0.003 0.016 2126 Dihedral : 5.011 25.788 2130 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.18), residues: 2115 helix: -0.44 (0.16), residues: 941 sheet: -0.11 (0.36), residues: 216 loop : -1.36 (0.21), residues: 958 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.458 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0960 time to fit residues: 8.7251 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.8510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 10482 Z= 0.402 Angle : 0.709 6.796 14554 Z= 0.453 Chirality : 0.054 0.148 1953 Planarity : 0.004 0.022 2126 Dihedral : 6.091 30.538 2130 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.51 % Favored : 87.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2115 helix: -1.26 (0.15), residues: 918 sheet: -0.40 (0.34), residues: 260 loop : -1.99 (0.20), residues: 937 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0960 time to fit residues: 8.5581 Evaluate side-chains 38 residues out of total 1815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 153 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.0370 chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 overall best weight: 1.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089149 restraints weight = 121923.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090717 restraints weight = 167302.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092102 restraints weight = 91115.442| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.009 10482 Z= 0.102 Angle : 0.379 4.369 14554 Z= 0.238 Chirality : 0.049 0.137 1953 Planarity : 0.002 0.012 2126 Dihedral : 4.158 20.507 2130 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % 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: -0.64 (0.19), residues: 2115 helix: 0.26 (0.17), residues: 969 sheet: 0.39 (0.40), residues: 190 loop : -1.27 (0.21), residues: 956 =============================================================================== Job complete usr+sys time: 1334.46 seconds wall clock time: 24 minutes 51.43 seconds (1491.43 seconds total)