Starting phenix.real_space_refine on Thu Jul 2 20:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.cif" model { file = "/net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7srr_25402/07_2026/7srr_25402.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1944 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5395 2.51 5 N 1411 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1713 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2518 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2072 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 61 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.59, per 1000 atoms: 0.19 Number of scatterers: 8394 At special positions: 0 Unit cell: (101.521, 117.139, 131.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1534 8.00 N 1411 7.00 C 5395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " distance=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 505.7 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 36.8% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.626A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.506A pdb=" N LEU B 134 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.255A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 183 through 204 removed outlier: 4.379A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.703A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.579A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.958A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.814A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.569A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.517A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'R' and resid 57 through 82 removed outlier: 3.998A pdb=" N MET R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) Proline residue: R 67 - end of helix removed outlier: 3.552A pdb=" N ILE R 76 " --> pdb=" O ASN R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 107 removed outlier: 3.610A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET R 94 " --> pdb=" O ASN R 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 117 removed outlier: 3.579A pdb=" N PHE R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 159 removed outlier: 3.794A pdb=" N LEU R 132 " --> pdb=" O CYS R 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE R 133 " --> pdb=" O PRO R 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER R 150 " --> pdb=" O LEU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 168 through 188 removed outlier: 3.737A pdb=" N ALA R 172 " --> pdb=" O SER R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 193 removed outlier: 3.999A pdb=" N ILE R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 193 " --> pdb=" O PRO R 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 188 through 193' Processing helix chain 'R' and resid 216 through 221 removed outlier: 3.625A pdb=" N PHE R 220 " --> pdb=" O ASP R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 245 removed outlier: 3.509A pdb=" N ILE R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR R 237 " --> pdb=" O MET R 233 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA R 243 " --> pdb=" O LEU R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 334 removed outlier: 3.760A pdb=" N ALA R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 323 " --> pdb=" O GLU R 319 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 350 Processing helix chain 'R' and resid 354 through 362 removed outlier: 3.508A pdb=" N LEU R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 371 Processing helix chain 'R' and resid 372 through 374 No H-bonds generated for 'chain 'R' and resid 372 through 374' Processing helix chain 'R' and resid 375 through 380 Processing helix chain 'R' and resid 384 through 392 Processing helix chain 'R' and resid 393 through 395 No H-bonds generated for 'chain 'R' and resid 393 through 395' Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.685A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.821A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.101A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.147A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 7.012A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 3.693A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.947A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.800A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.003A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.003A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.737A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1116 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: 1.13 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2674 1.34 - 1.46: 1849 1.46 - 1.58: 3977 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8579 Sorted by residual: bond pdb=" C14 7LD R 501 " pdb=" C16 7LD R 501 " ideal model delta sigma weight residual 1.525 1.403 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C11 7LD R 501 " pdb=" C9 7LD R 501 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C10 7LD R 501 " pdb=" C14 7LD R 501 " ideal model delta sigma weight residual 1.501 1.398 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C15 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.414 1.322 0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11357 1.72 - 3.44: 259 3.44 - 5.15: 57 5.15 - 6.87: 15 6.87 - 8.59: 6 Bond angle restraints: 11694 Sorted by residual: angle pdb=" N LYS R 247 " pdb=" CA LYS R 247 " pdb=" C LYS R 247 " ideal model delta sigma weight residual 112.57 104.65 7.92 1.13e+00 7.83e-01 4.91e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 113.23 105.54 7.69 1.24e+00 6.50e-01 3.85e+01 angle pdb=" N GLN R 320 " pdb=" CA GLN R 320 " pdb=" C GLN R 320 " ideal model delta sigma weight residual 113.88 106.26 7.62 1.23e+00 6.61e-01 3.84e+01 angle pdb=" C GLN R 320 " pdb=" CA GLN R 320 " pdb=" CB GLN R 320 " ideal model delta sigma weight residual 109.03 117.62 -8.59 1.62e+00 3.81e-01 2.81e+01 angle pdb=" N GLU R 319 " pdb=" CA GLU R 319 " pdb=" C GLU R 319 " ideal model delta sigma weight residual 113.17 106.59 6.58 1.26e+00 6.30e-01 2.73e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 4913 30.36 - 60.72: 98 60.72 - 91.07: 5 91.07 - 121.43: 0 121.43 - 151.79: 1 Dihedral angle restraints: 5017 sinusoidal: 1775 harmonic: 3242 Sorted by residual: dihedral pdb=" C16 7LD R 501 " pdb=" C17 7LD R 501 " pdb=" N3 7LD R 501 " pdb=" C18 7LD R 501 " ideal model delta sinusoidal sigma weight residual 91.75 -116.46 -151.79 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA GLU R 118 " pdb=" C GLU R 118 " pdb=" N ALA R 119 " pdb=" CA ALA R 119 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS B 73 " pdb=" C LYS B 73 " pdb=" N PHE B 74 " pdb=" CA PHE B 74 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1187 0.065 - 0.131: 172 0.131 - 0.196: 10 0.196 - 0.261: 3 0.261 - 0.326: 3 Chirality restraints: 1375 Sorted by residual: chirality pdb=" C14 7LD R 501 " pdb=" C10 7LD R 501 " pdb=" C13 7LD R 501 " pdb=" C16 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL R 325 " pdb=" CA VAL R 325 " pdb=" CG1 VAL R 325 " pdb=" CG2 VAL R 325 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 7LD R 501 " pdb=" C15 7LD R 501 " pdb=" C9 7LD R 501 " pdb=" N2 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1372 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 86 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C GLN R 86 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN R 86 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR R 87 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 325 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C VAL R 325 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL R 325 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 326 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 323 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C SER R 323 " -0.035 2.00e-02 2.50e+03 pdb=" O SER R 323 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS R 324 " 0.012 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 479 2.74 - 3.28: 7850 3.28 - 3.82: 12976 3.82 - 4.36: 15424 4.36 - 4.90: 27767 Nonbonded interactions: 64496 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.196 3.040 nonbonded pdb=" O ILE R 205 " pdb=" OG1 THR R 206 " model vdw 2.303 3.040 nonbonded pdb=" NE2 GLN C 75 " pdb=" O SER C 98 " model vdw 2.362 3.120 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG E 190 " pdb=" OD2 ASP E 211 " model vdw 2.374 3.120 ... (remaining 64491 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 8583 Z= 0.265 Angle : 0.670 8.591 11702 Z= 0.403 Chirality : 0.048 0.326 1375 Planarity : 0.004 0.046 1469 Dihedral : 12.519 151.787 2909 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1101 helix: 0.48 (0.29), residues: 377 sheet: 1.31 (0.33), residues: 275 loop : -0.96 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 213 TYR 0.023 0.001 TYR R 87 PHE 0.018 0.001 PHE R 133 TRP 0.011 0.001 TRP R 121 HIS 0.012 0.002 HIS R 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.27 ( 8579) covalent geometry : angle 0.66972 / 0.40 (11694) SS BOND : bond 0.00461 / 0.23 ( 4) SS BOND : angle 0.77480 / 0.41 ( 8) hydrogen bonds : bond 0.17546 / 11.97 ( 389) hydrogen bonds : angle 5.60377 / 4.07 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.342 Fit side-chains REVERT: B 199 ASP cc_start: 0.7359 (m-30) cc_final: 0.7092 (m-30) REVERT: C 188 MET cc_start: 0.8901 (mmm) cc_final: 0.8606 (mmm) REVERT: E 34 MET cc_start: 0.8697 (mmm) cc_final: 0.8419 (mmt) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.5085 time to fit residues: 88.6967 Evaluate side-chains 148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN C 293 ASN E 182 ASN R 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107595 restraints weight = 12254.729| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.61 r_work: 0.3204 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8583 Z= 0.150 Angle : 0.561 7.329 11702 Z= 0.296 Chirality : 0.044 0.153 1375 Planarity : 0.004 0.047 1469 Dihedral : 6.108 144.850 1195 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.76 % Allowed : 8.67 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1101 helix: 0.73 (0.29), residues: 380 sheet: 1.30 (0.32), residues: 282 loop : -0.80 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.013 0.001 TYR E 178 PHE 0.017 0.002 PHE B 74 TRP 0.011 0.001 TRP R 121 HIS 0.007 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8579) covalent geometry : angle 0.56031 / 0.30 (11694) SS BOND : bond 0.00582 / 0.29 ( 4) SS BOND : angle 1.35541 / 0.77 ( 8) hydrogen bonds : bond 0.05384 / 3.66 ( 389) hydrogen bonds : angle 4.24215 / 3.06 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.317 Fit side-chains REVERT: B 199 ASP cc_start: 0.7955 (m-30) cc_final: 0.7577 (m-30) REVERT: C 188 MET cc_start: 0.9002 (mmm) cc_final: 0.8785 (mmm) REVERT: C 217 MET cc_start: 0.8512 (pmm) cc_final: 0.8089 (pmm) outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 0.4699 time to fit residues: 76.2493 Evaluate side-chains 156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 0.0060 chunk 100 optimal weight: 0.0980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 ASN B 131 ASN C 293 ASN R 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108618 restraints weight = 12134.629| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.59 r_work: 0.3221 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8583 Z= 0.116 Angle : 0.513 6.204 11702 Z= 0.272 Chirality : 0.042 0.154 1375 Planarity : 0.004 0.048 1469 Dihedral : 5.693 129.387 1195 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.87 % Allowed : 9.72 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1101 helix: 0.99 (0.29), residues: 379 sheet: 1.27 (0.32), residues: 288 loop : -0.79 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.012 0.001 TYR E 178 PHE 0.014 0.001 PHE B 74 TRP 0.010 0.001 TRP R 121 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8579) covalent geometry : angle 0.51248 / 0.27 (11694) SS BOND : bond 0.00487 / 0.24 ( 4) SS BOND : angle 1.17221 / 0.68 ( 8) hydrogen bonds : bond 0.04600 / 3.12 ( 389) hydrogen bonds : angle 4.03041 / 2.91 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.319 Fit side-chains REVERT: B 73 LYS cc_start: 0.8283 (mmpt) cc_final: 0.8024 (mmpt) REVERT: B 199 ASP cc_start: 0.7965 (m-30) cc_final: 0.7614 (m-30) REVERT: C 52 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8364 (ptm160) REVERT: C 134 ARG cc_start: 0.8266 (mtm110) cc_final: 0.8040 (ptp-110) REVERT: C 188 MET cc_start: 0.9011 (mmm) cc_final: 0.8779 (mmm) REVERT: C 217 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8100 (pmm) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.5001 time to fit residues: 78.1619 Evaluate side-chains 153 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 7 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN B 116 ASN B 131 ASN C 293 ASN R 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107570 restraints weight = 12401.200| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.60 r_work: 0.3204 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8583 Z= 0.122 Angle : 0.520 7.562 11702 Z= 0.273 Chirality : 0.042 0.127 1375 Planarity : 0.004 0.048 1469 Dihedral : 5.373 112.851 1195 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.58 % Allowed : 11.48 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.26), residues: 1101 helix: 1.13 (0.29), residues: 380 sheet: 1.30 (0.32), residues: 288 loop : -0.78 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.012 0.001 TYR E 178 PHE 0.014 0.001 PHE B 74 TRP 0.010 0.001 TRP R 121 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8579) covalent geometry : angle 0.51949 / 0.27 (11694) SS BOND : bond 0.00511 / 0.26 ( 4) SS BOND : angle 1.15086 / 0.66 ( 8) hydrogen bonds : bond 0.04655 / 3.15 ( 389) hydrogen bonds : angle 3.96378 / 2.86 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.283 Fit side-chains REVERT: B 126 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8093 (ttmm) REVERT: B 199 ASP cc_start: 0.7988 (m-30) cc_final: 0.7660 (m-30) REVERT: C 52 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8317 (ptm160) REVERT: C 134 ARG cc_start: 0.8257 (mtm110) cc_final: 0.8024 (ptp-110) REVERT: C 188 MET cc_start: 0.9010 (mmm) cc_final: 0.8789 (mmm) REVERT: C 217 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8099 (pmm) outliers start: 22 outliers final: 13 residues processed: 157 average time/residue: 0.4630 time to fit residues: 77.7500 Evaluate side-chains 163 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 HIS B 101 ASN B 116 ASN B 131 ASN C 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104635 restraints weight = 12282.190| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.64 r_work: 0.3156 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8583 Z= 0.199 Angle : 0.597 8.944 11702 Z= 0.315 Chirality : 0.046 0.199 1375 Planarity : 0.004 0.048 1469 Dihedral : 5.363 97.744 1195 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.58 % Allowed : 12.65 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1101 helix: 1.00 (0.29), residues: 373 sheet: 1.25 (0.32), residues: 276 loop : -0.95 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.010 0.001 TYR E 178 PHE 0.018 0.002 PHE R 227 TRP 0.013 0.002 TRP R 121 HIS 0.008 0.002 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 ( 8579) covalent geometry : angle 0.59578 / 0.31 (11694) SS BOND : bond 0.00739 / 0.37 ( 4) SS BOND : angle 1.43261 / 0.79 ( 8) hydrogen bonds : bond 0.05895 / 3.98 ( 389) hydrogen bonds : angle 4.16636 / 3.00 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.205 Fit side-chains REVERT: B 31 ARG cc_start: 0.7240 (ttp80) cc_final: 0.6986 (ttp-170) REVERT: B 126 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7961 (ttmm) REVERT: B 199 ASP cc_start: 0.7957 (m-30) cc_final: 0.7648 (m-30) REVERT: B 222 GLU cc_start: 0.7425 (pp20) cc_final: 0.7195 (pp20) REVERT: C 52 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8315 (ptm160) REVERT: C 217 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8152 (pmm) REVERT: R 90 ASN cc_start: 0.8322 (m-40) cc_final: 0.7981 (m-40) REVERT: R 158 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8139 (tmtm) outliers start: 22 outliers final: 16 residues processed: 166 average time/residue: 0.4900 time to fit residues: 86.8329 Evaluate side-chains 171 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 HIS B 101 ASN B 116 ASN B 131 ASN C 16 ASN C 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104501 restraints weight = 12196.536| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.60 r_work: 0.3170 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8583 Z= 0.161 Angle : 0.571 7.536 11702 Z= 0.301 Chirality : 0.044 0.140 1375 Planarity : 0.004 0.050 1469 Dihedral : 5.049 83.760 1195 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.81 % Allowed : 14.17 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1101 helix: 1.07 (0.29), residues: 373 sheet: 1.32 (0.32), residues: 283 loop : -0.93 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 134 TYR 0.011 0.001 TYR E 178 PHE 0.015 0.002 PHE R 227 TRP 0.012 0.001 TRP R 121 HIS 0.007 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 8579) covalent geometry : angle 0.57015 / 0.30 (11694) SS BOND : bond 0.00613 / 0.31 ( 4) SS BOND : angle 1.32976 / 0.75 ( 8) hydrogen bonds : bond 0.05351 / 3.62 ( 389) hydrogen bonds : angle 4.08076 / 2.95 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.323 Fit side-chains REVERT: B 31 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6982 (ttp-170) REVERT: B 126 LYS cc_start: 0.8306 (ttmm) cc_final: 0.8006 (ttmm) REVERT: B 199 ASP cc_start: 0.7945 (m-30) cc_final: 0.7627 (m-30) REVERT: B 222 GLU cc_start: 0.7394 (pp20) cc_final: 0.7141 (pp20) REVERT: C 52 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8295 (ptm160) REVERT: C 217 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8180 (pmm) REVERT: R 90 ASN cc_start: 0.8310 (m-40) cc_final: 0.7987 (m-40) REVERT: R 158 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8083 (tmtm) outliers start: 24 outliers final: 15 residues processed: 163 average time/residue: 0.5001 time to fit residues: 87.2950 Evaluate side-chains 163 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 0.0040 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 68 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 95 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 overall best weight: 0.2470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 HIS B 101 ASN B 116 ASN B 131 ASN C 16 ASN C 88 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104156 restraints weight = 12321.879| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.63 r_work: 0.3213 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8583 Z= 0.104 Angle : 0.533 12.295 11702 Z= 0.277 Chirality : 0.042 0.182 1375 Planarity : 0.004 0.049 1469 Dihedral : 4.518 65.372 1195 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.22 % Allowed : 15.69 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1101 helix: 1.29 (0.29), residues: 382 sheet: 1.34 (0.32), residues: 281 loop : -0.80 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 134 TYR 0.013 0.001 TYR E 178 PHE 0.012 0.001 PHE B 74 TRP 0.010 0.001 TRP R 121 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 8579) covalent geometry : angle 0.53226 / 0.28 (11694) SS BOND : bond 0.00425 / 0.21 ( 4) SS BOND : angle 1.08583 / 0.63 ( 8) hydrogen bonds : bond 0.04110 / 2.79 ( 389) hydrogen bonds : angle 3.86434 / 2.79 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.364 Fit side-chains REVERT: B 31 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6915 (ttp-170) REVERT: B 126 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7932 (ttmm) REVERT: B 199 ASP cc_start: 0.7962 (m-30) cc_final: 0.7647 (m-30) REVERT: B 222 GLU cc_start: 0.7356 (pp20) cc_final: 0.7122 (pp20) REVERT: C 217 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8129 (pmm) REVERT: R 90 ASN cc_start: 0.8282 (m-40) cc_final: 0.7927 (m-40) outliers start: 19 outliers final: 13 residues processed: 149 average time/residue: 0.4999 time to fit residues: 79.4997 Evaluate side-chains 155 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 98 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 HIS B 116 ASN B 131 ASN C 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101208 restraints weight = 12190.530| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.56 r_work: 0.3158 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8583 Z= 0.196 Angle : 0.614 9.496 11702 Z= 0.318 Chirality : 0.045 0.143 1375 Planarity : 0.004 0.051 1469 Dihedral : 4.690 55.808 1195 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.46 % Allowed : 15.81 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1101 helix: 1.05 (0.29), residues: 379 sheet: 1.22 (0.32), residues: 280 loop : -0.86 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 134 TYR 0.010 0.001 TYR E 178 PHE 0.018 0.002 PHE R 227 TRP 0.012 0.001 TRP R 121 HIS 0.008 0.002 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 ( 8579) covalent geometry : angle 0.61310 / 0.32 (11694) SS BOND : bond 0.00715 / 0.35 ( 4) SS BOND : angle 1.40783 / 0.78 ( 8) hydrogen bonds : bond 0.05827 / 3.93 ( 389) hydrogen bonds : angle 4.09945 / 2.96 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.316 Fit side-chains REVERT: B 31 ARG cc_start: 0.7219 (ttp80) cc_final: 0.7007 (ttp-170) REVERT: B 199 ASP cc_start: 0.7952 (m-30) cc_final: 0.7642 (m-30) REVERT: B 222 GLU cc_start: 0.7387 (pp20) cc_final: 0.7081 (pp20) REVERT: C 217 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8240 (pmm) REVERT: R 90 ASN cc_start: 0.8299 (m-40) cc_final: 0.7986 (m-40) REVERT: R 158 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8096 (tmtm) outliers start: 21 outliers final: 17 residues processed: 164 average time/residue: 0.4591 time to fit residues: 80.7287 Evaluate side-chains 169 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 106 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 HIS B 116 ASN B 131 ASN C 16 ASN C 142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105372 restraints weight = 12145.674| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.54 r_work: 0.3201 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8583 Z= 0.133 Angle : 0.560 10.683 11702 Z= 0.292 Chirality : 0.043 0.213 1375 Planarity : 0.004 0.055 1469 Dihedral : 4.472 49.459 1195 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.34 % Allowed : 16.63 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1101 helix: 1.20 (0.29), residues: 379 sheet: 1.31 (0.32), residues: 286 loop : -0.79 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 134 TYR 0.011 0.001 TYR E 178 PHE 0.013 0.001 PHE R 227 TRP 0.011 0.001 TRP R 121 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8579) covalent geometry : angle 0.55926 / 0.29 (11694) SS BOND : bond 0.00526 / 0.26 ( 4) SS BOND : angle 1.15268 / 0.66 ( 8) hydrogen bonds : bond 0.04824 / 3.26 ( 389) hydrogen bonds : angle 3.97032 / 2.87 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.336 Fit side-chains REVERT: B 31 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6951 (ttp80) REVERT: B 199 ASP cc_start: 0.7941 (m-30) cc_final: 0.7609 (m-30) REVERT: B 222 GLU cc_start: 0.7320 (pp20) cc_final: 0.7004 (pp20) REVERT: C 217 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8168 (pmm) REVERT: R 90 ASN cc_start: 0.8260 (m-40) cc_final: 0.7925 (m-40) REVERT: R 158 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8018 (tmtm) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.4819 time to fit residues: 82.2212 Evaluate side-chains 167 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 HIS B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105050 restraints weight = 12094.250| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.78 r_work: 0.3173 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8583 Z= 0.143 Angle : 0.575 10.417 11702 Z= 0.298 Chirality : 0.043 0.142 1375 Planarity : 0.004 0.059 1469 Dihedral : 4.435 44.824 1195 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.22 % Allowed : 16.98 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1101 helix: 1.21 (0.29), residues: 379 sheet: 1.30 (0.31), residues: 286 loop : -0.78 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 134 TYR 0.011 0.001 TYR E 178 PHE 0.014 0.001 PHE R 227 TRP 0.011 0.001 TRP R 121 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 8579) covalent geometry : angle 0.57480 / 0.30 (11694) SS BOND : bond 0.00558 / 0.28 ( 4) SS BOND : angle 1.17574 / 0.66 ( 8) hydrogen bonds : bond 0.04991 / 3.37 ( 389) hydrogen bonds : angle 3.98308 / 2.88 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.327 Fit side-chains REVERT: B 31 ARG cc_start: 0.7260 (ttp80) cc_final: 0.7040 (ttp80) REVERT: B 199 ASP cc_start: 0.7968 (m-30) cc_final: 0.7646 (m-30) REVERT: B 222 GLU cc_start: 0.7413 (pp20) cc_final: 0.7053 (pp20) REVERT: C 217 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8233 (pmm) REVERT: R 90 ASN cc_start: 0.8283 (m-40) cc_final: 0.7950 (m-40) REVERT: R 158 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8063 (tmtm) outliers start: 19 outliers final: 16 residues processed: 159 average time/residue: 0.4854 time to fit residues: 82.6516 Evaluate side-chains 168 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.0050 chunk 96 optimal weight: 0.9980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 HIS B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106978 restraints weight = 12231.267| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.60 r_work: 0.3196 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8583 Z= 0.119 Angle : 0.551 10.010 11702 Z= 0.286 Chirality : 0.043 0.233 1375 Planarity : 0.004 0.059 1469 Dihedral : 4.268 35.999 1195 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.22 % Allowed : 16.98 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1101 helix: 1.32 (0.29), residues: 382 sheet: 1.31 (0.31), residues: 286 loop : -0.78 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 134 TYR 0.011 0.001 TYR E 178 PHE 0.013 0.001 PHE B 74 TRP 0.011 0.001 TRP R 121 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8579) covalent geometry : angle 0.55068 / 0.29 (11694) SS BOND : bond 0.00480 / 0.24 ( 4) SS BOND : angle 1.06205 / 0.61 ( 8) hydrogen bonds : bond 0.04463 / 3.01 ( 389) hydrogen bonds : angle 3.90402 / 2.82 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3413.38 seconds wall clock time: 58 minutes 45.94 seconds (3525.94 seconds total)