Starting phenix.real_space_refine on Fri Feb 14 17:08:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u68_20662/02_2025/6u68_20662.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u68_20662/02_2025/6u68_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/cci-nas-00/data/ceres_data/6u68_20662/02_2025/6u68_20662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u68_20662/02_2025/6u68_20662.map" model { file = "/net/cci-nas-00/data/ceres_data/6u68_20662/02_2025/6u68_20662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u68_20662/02_2025/6u68_20662.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 10.70, per 1000 atoms: 1.02 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 - 3.00 Amino acid : True - 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: 2.89 Conformation dependent library (CDL) restraints added in 3.1 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: 1.77 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: 3.89 Time building geometry restraints manager: 3.30 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: 0.00 - 2.77: 14255 2.77 - 5.54: 269 5.54 - 8.30: 29 8.30 - 11.07: 0 11.07 - 13.84: 1 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 Time spend for trying shortcut: 0.00 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 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.300 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 % Allowed : 0.00 % Favored : 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.920 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1011 time to fit residues: 8.5555 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.108779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091898 restraints weight = 121145.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093417 restraints weight = 131753.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094669 restraints weight = 91654.112| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5097 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= 0.396 Angle : 0.849 6.694 14554 Z= 0.539 Chirality : 0.054 0.137 1953 Planarity : 0.006 0.024 2126 Dihedral : 6.126 25.611 2130 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -1.98 (0.17), residues: 2115 helix: -1.65 (0.14), residues: 961 sheet: 0.40 (0.31), residues: 268 loop : -1.29 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0999 time to fit residues: 8.8384 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 187 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 209 optimal weight: 9.9990 chunk 162 optimal weight: 0.1980 overall best weight: 2.0382 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.123196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109880 restraints weight = 118216.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110120 restraints weight = 119335.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110296 restraints weight = 93104.089| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10482 Z= 0.123 Angle : 0.384 4.218 14554 Z= 0.243 Chirality : 0.049 0.136 1953 Planarity : 0.002 0.011 2126 Dihedral : 3.810 17.587 2130 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -0.52 (0.18), residues: 2115 helix: -0.05 (0.16), residues: 1005 sheet: 0.74 (0.32), residues: 258 loop : -0.93 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0905 time to fit residues: 8.1290 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.104750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089988 restraints weight = 101828.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089942 restraints weight = 118457.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090527 restraints weight = 105831.156| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10482 Z= 0.279 Angle : 0.607 4.729 14554 Z= 0.386 Chirality : 0.052 0.138 1953 Planarity : 0.004 0.020 2126 Dihedral : 5.152 23.610 2130 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -0.90 (0.18), residues: 2115 helix: -0.45 (0.16), residues: 983 sheet: 0.35 (0.31), residues: 266 loop : -0.92 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0928 time to fit residues: 8.3138 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 131 optimal weight: 8.9990 chunk 207 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 208 optimal weight: 40.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.099440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.085432 restraints weight = 96750.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.085258 restraints weight = 123333.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085856 restraints weight = 108364.148| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 10482 Z= 0.440 Angle : 0.786 6.999 14554 Z= 0.502 Chirality : 0.055 0.146 1953 Planarity : 0.005 0.022 2126 Dihedral : 6.517 31.886 2130 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.95 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -2.28 (0.17), residues: 2115 helix: -1.47 (0.15), residues: 968 sheet: -0.39 (0.32), residues: 265 loop : -1.76 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0930 time to fit residues: 8.3223 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 22 optimal weight: 0.0060 chunk 82 optimal weight: 1.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.113416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102521 restraints weight = 100482.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103644 restraints weight = 168801.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104991 restraints weight = 86239.798| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.7577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 10482 Z= 0.157 Angle : 0.428 4.351 14554 Z= 0.273 Chirality : 0.050 0.138 1953 Planarity : 0.002 0.016 2126 Dihedral : 4.582 21.684 2130 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -0.90 (0.18), residues: 2115 helix: -0.10 (0.16), residues: 948 sheet: -0.04 (0.36), residues: 206 loop : -1.15 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1010 time to fit residues: 8.5936 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 105 optimal weight: 0.0670 chunk 174 optimal weight: 0.9980 chunk 90 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.7722 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.114125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103324 restraints weight = 106175.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105655 restraints weight = 175953.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105678 restraints weight = 75474.580| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.7615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 10482 Z= 0.144 Angle : 0.401 3.462 14554 Z= 0.255 Chirality : 0.050 0.134 1953 Planarity : 0.002 0.015 2126 Dihedral : 4.009 19.048 2130 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -0.32 (0.19), residues: 2115 helix: 0.55 (0.17), residues: 967 sheet: 0.06 (0.35), residues: 216 loop : -1.04 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1003 time to fit residues: 8.9393 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 116 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 113 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.117310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105101 restraints weight = 121428.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105633 restraints weight = 115181.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105209 restraints weight = 84855.783| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.7532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 10482 Z= 0.085 Angle : 0.336 3.161 14554 Z= 0.211 Chirality : 0.049 0.134 1953 Planarity : 0.001 0.013 2126 Dihedral : 3.395 16.050 2130 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 0.47 (0.19), residues: 2115 helix: 1.31 (0.18), residues: 953 sheet: 0.56 (0.37), residues: 198 loop : -0.74 (0.22), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.155 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0977 time to fit residues: 8.6492 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 139 optimal weight: 0.5980 chunk 190 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 60 optimal weight: 50.0000 chunk 73 optimal weight: 9.9990 overall best weight: 5.6986 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.101551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085958 restraints weight = 113257.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.087189 restraints weight = 156233.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088288 restraints weight = 95778.001| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.7982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10482 Z= 0.272 Angle : 0.551 5.053 14554 Z= 0.352 Chirality : 0.051 0.137 1953 Planarity : 0.003 0.020 2126 Dihedral : 4.764 24.450 2130 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.91 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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 (0.18), residues: 2115 helix: 0.26 (0.17), residues: 940 sheet: -0.07 (0.36), residues: 217 loop : -1.15 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0952 time to fit residues: 8.7463 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 177 optimal weight: 0.0270 chunk 52 optimal weight: 6.9990 overall best weight: 3.7244 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.103151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087762 restraints weight = 116392.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.089272 restraints weight = 155789.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.090238 restraints weight = 91365.009| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 10482 Z= 0.185 Angle : 0.439 4.010 14554 Z= 0.280 Chirality : 0.050 0.135 1953 Planarity : 0.002 0.017 2126 Dihedral : 4.266 22.169 2130 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -0.41 (0.19), residues: 2115 helix: 0.52 (0.17), residues: 949 sheet: 0.04 (0.37), residues: 214 loop : -1.12 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 ********************** 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 to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.144 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1019 time to fit residues: 8.8709 Evaluate side-chains 38 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 92 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 208 optimal weight: 40.0000 chunk 42 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 overall best weight: 3.4584 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.103354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.088105 restraints weight = 120971.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.089962 restraints weight = 155688.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.091026 restraints weight = 87096.187| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.8095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 10482 Z= 0.172 Angle : 0.424 3.740 14554 Z= 0.270 Chirality : 0.050 0.134 1953 Planarity : 0.002 0.016 2126 Dihedral : 4.114 20.887 2130 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -0.36 (0.19), residues: 2115 helix: 0.62 (0.17), residues: 949 sheet: 0.17 (0.34), residues: 254 loop : -1.25 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.10 seconds wall clock time: 43 minutes 50.54 seconds (2630.54 seconds total)