Starting phenix.real_space_refine on Mon Jul 28 14:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u68_20662/07_2025/6u68_20662.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u68_20662/07_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_20662/07_2025/6u68_20662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u68_20662/07_2025/6u68_20662.map" model { file = "/net/cci-nas-00/data/ceres_data/6u68_20662/07_2025/6u68_20662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u68_20662/07_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-5711/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: 11.08, per 1000 atoms: 1.06 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: 2.92 Conformation dependent library (CDL) restraints added in 3.3 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: 1.69 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: 3.60 Time building geometry restraints manager: 3.39 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: 0.570 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 35.460 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.000 ------------------------------------------------------------------------------- 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= 0.430 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 Details of bonding type rmsd hydrogen bonds : bond 0.27242 ( 666) hydrogen bonds : angle 8.88189 ( 1929) covalent geometry : bond 0.00567 (10482) covalent geometry : angle 0.89523 (14554) *********************** 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 : 1.166 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0920 time to fit residues: 8.1661 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 : 1.070 ------------------------------------------------------------------------------- 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 = 121144.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093361 restraints weight = 131723.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094654 restraints weight = 92062.490| |-----------------------------------------------------------------------------| 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: 0.5096 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= 0.389 Angle : 0.849 6.695 14554 Z= 0.540 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 Details of bonding type rmsd hydrogen bonds : bond 0.06480 ( 666) hydrogen bonds : angle 6.91919 ( 1929) covalent geometry : bond 0.00536 (10482) covalent geometry : angle 0.84897 (14554) *********************** 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 : 1.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0933 time to fit residues: 8.2887 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 : 1.276 ------------------------------------------------------------------------------- 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: 10.0000 chunk 166 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.119264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106275 restraints weight = 118808.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106645 restraints weight = 108631.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106584 restraints weight = 82286.267| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10482 Z= 0.194 Angle : 0.477 4.441 14554 Z= 0.303 Chirality : 0.050 0.137 1953 Planarity : 0.003 0.015 2126 Dihedral : 4.322 19.132 2130 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -0.77 (0.18), residues: 2115 helix: -0.28 (0.16), residues: 995 sheet: 0.89 (0.35), residues: 216 loop : -1.02 (0.21), residues: 904 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 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 666) hydrogen bonds : angle 5.36573 ( 1929) covalent geometry : bond 0.00265 (10482) covalent geometry : angle 0.47683 (14554) *********************** 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 : 1.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0953 time to fit residues: 8.4511 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 : 1.183 ------------------------------------------------------------------------------- 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: 2.9990 chunk 35 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 138 optimal weight: 0.0670 chunk 4 optimal weight: 0.0980 chunk 60 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 overall best weight: 3.4324 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.115772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104309 restraints weight = 101943.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105573 restraints weight = 177512.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106463 restraints weight = 115737.550| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 10482 Z= 0.188 Angle : 0.460 3.913 14554 Z= 0.294 Chirality : 0.050 0.134 1953 Planarity : 0.003 0.015 2126 Dihedral : 4.174 20.344 2130 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.60 % 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: -0.03 (0.19), residues: 2115 helix: 0.45 (0.17), residues: 995 sheet: 0.67 (0.31), residues: 266 loop : -0.69 (0.22), residues: 854 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 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 666) hydrogen bonds : angle 5.23332 ( 1929) covalent geometry : bond 0.00257 (10482) covalent geometry : angle 0.46006 (14554) *********************** 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 : 1.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0932 time to fit residues: 8.1962 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 : 1.114 ------------------------------------------------------------------------------- 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: 10.0000 chunk 207 optimal weight: 0.2980 chunk 154 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 208 optimal weight: 30.0000 overall best weight: 6.8588 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.101610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.087460 restraints weight = 95631.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087418 restraints weight = 116103.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087863 restraints weight = 104555.887| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 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 = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.7448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10482 Z= 0.316 Angle : 0.648 5.846 14554 Z= 0.413 Chirality : 0.053 0.141 1953 Planarity : 0.004 0.022 2126 Dihedral : 5.566 28.762 2130 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % 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: -1.25 (0.18), residues: 2115 helix: -0.55 (0.16), residues: 968 sheet: -0.05 (0.34), residues: 225 loop : -1.23 (0.21), residues: 922 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 Details of bonding type rmsd hydrogen bonds : bond 0.05824 ( 666) hydrogen bonds : angle 6.81323 ( 1929) covalent geometry : bond 0.00436 (10482) covalent geometry : angle 0.64850 (14554) *********************** 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 : 1.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0949 time to fit residues: 8.3065 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 : 1.125 ------------------------------------------------------------------------------- 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: 7.9990 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.102524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088267 restraints weight = 100460.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088513 restraints weight = 116119.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088992 restraints weight = 101641.478| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.7664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10482 Z= 0.253 Angle : 0.528 5.219 14554 Z= 0.337 Chirality : 0.051 0.140 1953 Planarity : 0.003 0.019 2126 Dihedral : 4.976 25.036 2130 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % 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: -0.98 (0.18), residues: 2115 helix: -0.21 (0.16), residues: 951 sheet: -0.01 (0.36), residues: 213 loop : -1.17 (0.21), residues: 951 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 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 666) hydrogen bonds : angle 6.14895 ( 1929) covalent geometry : bond 0.00347 (10482) covalent geometry : angle 0.52752 (14554) *********************** 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 : 1.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0917 time to fit residues: 8.1692 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 : 1.063 ------------------------------------------------------------------------------- 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: 0.1980 chunk 127 optimal weight: 0.0870 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 105 optimal weight: 0.0870 chunk 174 optimal weight: 0.7980 chunk 90 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.118111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106593 restraints weight = 105531.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.109343 restraints weight = 172397.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109750 restraints weight = 73660.392| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.7392 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= 0.076 Angle : 0.343 3.401 14554 Z= 0.215 Chirality : 0.048 0.136 1953 Planarity : 0.001 0.012 2126 Dihedral : 3.539 18.054 2130 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 1.18 (0.17), residues: 954 sheet: 0.48 (0.38), residues: 196 loop : -0.66 (0.21), residues: 965 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 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 666) hydrogen bonds : angle 4.55271 ( 1929) covalent geometry : bond 0.00100 (10482) covalent geometry : angle 0.34340 (14554) *********************** 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 : 1.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0988 time to fit residues: 8.9127 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 : 1.238 ------------------------------------------------------------------------------- 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: 5.9990 chunk 174 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 31 optimal weight: 0.2980 chunk 4 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.110935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097867 restraints weight = 118709.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099191 restraints weight = 176716.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100669 restraints weight = 103767.489| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.7658 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= 0.194 Angle : 0.447 3.850 14554 Z= 0.285 Chirality : 0.050 0.134 1953 Planarity : 0.002 0.017 2126 Dihedral : 4.108 21.105 2130 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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: -0.03 (0.19), residues: 2115 helix: 0.79 (0.17), residues: 952 sheet: 0.22 (0.36), residues: 216 loop : -0.86 (0.21), residues: 947 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 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 666) hydrogen bonds : angle 5.37787 ( 1929) covalent geometry : bond 0.00266 (10482) covalent geometry : angle 0.44739 (14554) *********************** 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 : 1.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0915 time to fit residues: 8.1111 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 : 1.148 ------------------------------------------------------------------------------- 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: 2.9990 chunk 190 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 21 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 0.0570 chunk 170 optimal weight: 10.0000 chunk 60 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 overall best weight: 2.8704 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.104784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088815 restraints weight = 112312.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.089933 restraints weight = 141618.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091135 restraints weight = 99434.757| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.7701 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= 0.146 Angle : 0.394 3.590 14554 Z= 0.250 Chirality : 0.049 0.134 1953 Planarity : 0.002 0.015 2126 Dihedral : 3.874 20.148 2130 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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: 0.17 (0.19), residues: 2115 helix: 1.02 (0.17), residues: 952 sheet: 0.26 (0.36), residues: 216 loop : -0.81 (0.22), residues: 947 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 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 666) hydrogen bonds : angle 5.05608 ( 1929) covalent geometry : bond 0.00199 (10482) covalent geometry : angle 0.39400 (14554) *********************** 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 : 1.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0938 time to fit residues: 8.4322 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 : 1.317 ------------------------------------------------------------------------------- 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: 10.0000 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 186 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.103616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087696 restraints weight = 116190.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.088715 restraints weight = 150973.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089885 restraints weight = 99913.014| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.7926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 10482 Z= 0.178 Angle : 0.434 3.711 14554 Z= 0.276 Chirality : 0.050 0.134 1953 Planarity : 0.002 0.017 2126 Dihedral : 4.122 21.323 2130 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % 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: -0.08 (0.19), residues: 2115 helix: 0.79 (0.17), residues: 952 sheet: 0.13 (0.37), residues: 216 loop : -0.92 (0.22), residues: 947 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 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 666) hydrogen bonds : angle 5.39032 ( 1929) covalent geometry : bond 0.00244 (10482) covalent geometry : angle 0.43362 (14554) ********************** 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 : 1.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0924 time to fit residues: 8.1881 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 : 1.139 ------------------------------------------------------------------------------- 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: 1.9990 chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 50.0000 chunk 42 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.102316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.086895 restraints weight = 121261.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088521 restraints weight = 164242.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089449 restraints weight = 93363.776| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.8122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 10482 Z= 0.230 Angle : 0.494 4.596 14554 Z= 0.315 Chirality : 0.051 0.136 1953 Planarity : 0.002 0.018 2126 Dihedral : 4.478 23.747 2130 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % 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: -0.48 (0.19), residues: 2115 helix: 0.43 (0.17), residues: 950 sheet: 0.14 (0.34), residues: 255 loop : -1.21 (0.22), residues: 910 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 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 666) hydrogen bonds : angle 5.79733 ( 1929) covalent geometry : bond 0.00316 (10482) covalent geometry : angle 0.49415 (14554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.29 seconds wall clock time: 47 minutes 3.01 seconds (2823.01 seconds total)