Starting phenix.real_space_refine on Thu Mar 5 10:25:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bto_30180/03_2026/7bto_30180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bto_30180/03_2026/7bto_30180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bto_30180/03_2026/7bto_30180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bto_30180/03_2026/7bto_30180.map" model { file = "/net/cci-nas-00/data/ceres_data/7bto_30180/03_2026/7bto_30180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bto_30180/03_2026/7bto_30180.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 984 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 46 5.16 5 C 13618 2.51 5 N 3506 2.21 5 O 4113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21283 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3693 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 17, 'PTRANS': 13, 'TRANS': 438} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3691 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 17, 'PTRANS': 13, 'TRANS': 438} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1334 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "E" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1334 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "F" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3574 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 9, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3574 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 9, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Chain: "C" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 490 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.28, per 1000 atoms: 0.20 Number of scatterers: 21283 At special positions: 0 Unit cell: (163.35, 149.85, 148.5, 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 46 16.00 O 4113 8.00 N 3506 7.00 C 13618 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 39.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.605A pdb=" N GLN A 15 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 54 removed outlier: 3.534A pdb=" N PHE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN A 34 " --> pdb=" O TRP A 30 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.908A pdb=" N GLY A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 163 Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.036A pdb=" N TYR A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.724A pdb=" N LEU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 335 through 346 removed outlier: 3.638A pdb=" N TYR A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 378 removed outlier: 4.037A pdb=" N ILE A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 378 " --> pdb=" O TYR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 482 through 507 removed outlier: 3.714A pdb=" N ALA A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.544A pdb=" N VAL B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 54 removed outlier: 3.534A pdb=" N PHE B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN B 34 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 removed outlier: 4.343A pdb=" N TYR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.910A pdb=" N GLY B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 163 Processing helix chain 'B' and resid 177 through 186 removed outlier: 4.035A pdb=" N TYR B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.725A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.639A pdb=" N TYR B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 removed outlier: 4.025A pdb=" N ILE B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN B 378 " --> pdb=" O TYR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 482 through 507 removed outlier: 3.662A pdb=" N ALA B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.786A pdb=" N VAL D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.639A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 131 through 136 removed outlier: 4.159A pdb=" N ASN D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.786A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 3.639A pdb=" N GLU E 71 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 112 through 123 Processing helix chain 'E' and resid 131 through 136 removed outlier: 4.159A pdb=" N ASN E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 151 Processing helix chain 'F' and resid 34 through 47 Processing helix chain 'F' and resid 57 through 73 removed outlier: 3.612A pdb=" N LEU F 61 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.584A pdb=" N TRP F 81 " --> pdb=" O ASN F 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 172 through 180 removed outlier: 4.029A pdb=" N PHE F 177 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 removed outlier: 3.612A pdb=" N TYR F 197 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 248 removed outlier: 3.538A pdb=" N PHE F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 273 through 292 removed outlier: 3.532A pdb=" N THR F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 removed outlier: 3.508A pdb=" N GLU F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 353 Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 383 through 391 Processing helix chain 'F' and resid 416 through 426 Processing helix chain 'G' and resid 34 through 47 Processing helix chain 'G' and resid 57 through 73 removed outlier: 3.624A pdb=" N LEU G 61 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 71 " --> pdb=" O GLN G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 88 removed outlier: 3.581A pdb=" N TRP G 81 " --> pdb=" O ASN G 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 172 through 180 removed outlier: 4.043A pdb=" N PHE G 177 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 197 removed outlier: 3.615A pdb=" N TYR G 197 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 248 removed outlier: 3.539A pdb=" N PHE G 248 " --> pdb=" O THR G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 273 through 292 removed outlier: 3.541A pdb=" N THR G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 removed outlier: 3.507A pdb=" N GLU G 326 " --> pdb=" O ARG G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 353 Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 383 through 391 Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'I' and resid 20 through 24 removed outlier: 3.601A pdb=" N GLU I 23 " --> pdb=" O PRO I 20 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I 24 " --> pdb=" O LEU I 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 20 through 24' Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'I' and resid 134 through 141 removed outlier: 3.621A pdb=" N TYR I 138 " --> pdb=" O TRP I 134 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS I 141 " --> pdb=" O ASN I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 158 Processing helix chain 'I' and resid 158 through 193 removed outlier: 3.673A pdb=" N ASP I 191 " --> pdb=" O ASN I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 259 removed outlier: 3.936A pdb=" N VAL I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER I 259 " --> pdb=" O VAL I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 318 Processing helix chain 'I' and resid 318 through 326 removed outlier: 4.698A pdb=" N ARG I 324 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA I 326 " --> pdb=" O ILE I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 343 removed outlier: 3.830A pdb=" N LEU I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 356 removed outlier: 4.053A pdb=" N GLN I 355 " --> pdb=" O ILE I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 369 removed outlier: 3.530A pdb=" N LEU I 367 " --> pdb=" O LYS I 363 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN I 369 " --> pdb=" O ASP I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 391 Processing helix chain 'C' and resid 975 through 990 Processing helix chain 'C' and resid 998 through 1003 removed outlier: 3.654A pdb=" N LEU C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'H' and resid 975 through 990 Processing helix chain 'H' and resid 1016 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 300 removed outlier: 6.685A pdb=" N PHE A 296 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LYS A 350 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA A 298 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 352 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 300 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 354 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 399 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 387 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A 405 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 381 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 253 through 254 Processing sheet with id=AA4, first strand: chain 'B' and resid 296 through 300 removed outlier: 6.686A pdb=" N PHE B 296 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS B 350 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA B 298 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 352 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 300 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 354 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 399 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 387 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER B 405 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL B 381 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.887A pdb=" N ASP D 50 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 104 through 107 Processing sheet with id=AA7, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.888A pdb=" N ASP E 50 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 104 through 107 Processing sheet with id=AA9, first strand: chain 'F' and resid 108 through 112 Processing sheet with id=AB1, first strand: chain 'F' and resid 134 through 138 removed outlier: 6.026A pdb=" N VAL F 156 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU F 200 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 163 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 261 through 264 Processing sheet with id=AB3, first strand: chain 'F' and resid 358 through 359 removed outlier: 6.233A pdb=" N VAL F 333 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR F 381 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE F 335 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS F 332 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE F 406 " --> pdb=" O LYS F 332 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE F 334 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL F 403 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE F 432 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N PHE F 405 " --> pdb=" O PHE F 432 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE F 434 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE F 407 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY F 303 " --> pdb=" O GLN F 431 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY F 433 " --> pdb=" O GLY F 303 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS F 307 " --> pdb=" O THR F 435 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR F 304 " --> pdb=" O LEU F 458 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER F 460 " --> pdb=" O TYR F 304 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP F 306 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 108 through 112 Processing sheet with id=AB5, first strand: chain 'G' and resid 134 through 138 removed outlier: 6.024A pdb=" N VAL G 156 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 200 " --> pdb=" O LEU G 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN G 163 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 261 through 264 Processing sheet with id=AB7, first strand: chain 'G' and resid 358 through 359 removed outlier: 6.232A pdb=" N VAL G 333 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR G 381 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE G 335 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS G 332 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE G 406 " --> pdb=" O LYS G 332 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE G 334 " --> pdb=" O ILE G 406 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL G 403 " --> pdb=" O TYR G 430 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE G 432 " --> pdb=" O VAL G 403 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE G 405 " --> pdb=" O PHE G 432 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE G 434 " --> pdb=" O PHE G 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE G 407 " --> pdb=" O PHE G 434 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY G 303 " --> pdb=" O GLN G 431 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY G 433 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS G 307 " --> pdb=" O THR G 435 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR G 304 " --> pdb=" O LEU G 458 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER G 460 " --> pdb=" O TYR G 304 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP G 306 " --> pdb=" O SER G 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=AB9, first strand: chain 'I' and resid 26 through 28 removed outlier: 3.888A pdb=" N LYS I 99 " --> pdb=" O ILE I 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 46 through 48 removed outlier: 6.234A pdb=" N ILE I 46 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY I 58 " --> pdb=" O ILE I 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 202 through 205 Processing sheet with id=AC3, first strand: chain 'I' and resid 249 through 251 removed outlier: 4.275A pdb=" N ASP I 249 " --> pdb=" O TRP I 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 285 through 287 730 hydrogen bonds defined for protein. 2115 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: 3.42 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5962 1.33 - 1.46: 4385 1.46 - 1.58: 11300 1.58 - 1.70: 1 1.70 - 1.82: 78 Bond restraints: 21726 Sorted by residual: bond pdb=" C ASN C1010 " pdb=" N PRO C1011 " ideal model delta sigma weight residual 1.334 1.420 -0.086 2.34e-02 1.83e+03 1.36e+01 bond pdb=" C ASN H1010 " pdb=" N PRO H1011 " ideal model delta sigma weight residual 1.334 1.419 -0.085 2.34e-02 1.83e+03 1.33e+01 bond pdb=" CA ILE B 430 " pdb=" CB ILE B 430 " ideal model delta sigma weight residual 1.540 1.605 -0.065 2.70e-02 1.37e+03 5.84e+00 bond pdb=" C SER C1007 " pdb=" N PRO C1008 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.51e+00 bond pdb=" C SER H1007 " pdb=" N PRO H1008 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.62e+00 ... (remaining 21721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 28716 3.06 - 6.12: 552 6.12 - 9.18: 99 9.18 - 12.24: 30 12.24 - 15.30: 5 Bond angle restraints: 29402 Sorted by residual: angle pdb=" N LYS A 98 " pdb=" CA LYS A 98 " pdb=" C LYS A 98 " ideal model delta sigma weight residual 110.80 96.25 14.55 2.13e+00 2.20e-01 4.66e+01 angle pdb=" C SER G 266 " pdb=" N GLN G 267 " pdb=" CA GLN G 267 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C SER F 266 " pdb=" N GLN F 267 " pdb=" CA GLN F 267 " ideal model delta sigma weight residual 121.70 133.62 -11.92 1.80e+00 3.09e-01 4.38e+01 angle pdb=" C THR B 409 " pdb=" N ASP B 410 " pdb=" CA ASP B 410 " ideal model delta sigma weight residual 121.70 132.42 -10.72 1.80e+00 3.09e-01 3.55e+01 angle pdb=" C ALA A 97 " pdb=" N LYS A 98 " pdb=" CA LYS A 98 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 ... (remaining 29397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 11924 15.17 - 30.34: 814 30.34 - 45.51: 216 45.51 - 60.68: 11 60.68 - 75.85: 22 Dihedral angle restraints: 12987 sinusoidal: 5206 harmonic: 7781 Sorted by residual: dihedral pdb=" CA LYS A 80 " pdb=" C LYS A 80 " pdb=" N THR A 81 " pdb=" CA THR A 81 " ideal model delta harmonic sigma weight residual 180.00 125.45 54.55 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA LYS B 80 " pdb=" C LYS B 80 " pdb=" N THR B 81 " pdb=" CA THR B 81 " ideal model delta harmonic sigma weight residual 180.00 125.62 54.38 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA VAL A 474 " pdb=" C VAL A 474 " pdb=" N GLU A 475 " pdb=" CA GLU A 475 " ideal model delta harmonic sigma weight residual 180.00 135.81 44.19 0 5.00e+00 4.00e-02 7.81e+01 ... (remaining 12984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2619 0.075 - 0.150: 549 0.150 - 0.225: 67 0.225 - 0.300: 14 0.300 - 0.375: 6 Chirality restraints: 3255 Sorted by residual: chirality pdb=" CB ILE A 310 " pdb=" CA ILE A 310 " pdb=" CG1 ILE A 310 " pdb=" CG2 ILE A 310 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE B 310 " pdb=" CA ILE B 310 " pdb=" CG1 ILE B 310 " pdb=" CG2 ILE B 310 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 3252 not shown) Planarity restraints: 3796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C1007 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C1008 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C1008 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C1008 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 72 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO I 73 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO I 73 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 73 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 46 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO I 47 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 47 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 47 " -0.042 5.00e-02 4.00e+02 ... (remaining 3793 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 124 2.53 - 3.13: 15875 3.13 - 3.72: 32760 3.72 - 4.31: 44449 4.31 - 4.90: 71171 Nonbonded interactions: 164379 Sorted by model distance: nonbonded pdb=" ND2 ASN B 390 " pdb=" O THR B 395 " model vdw 1.943 3.120 nonbonded pdb=" O ALA I 255 " pdb=" OG SER I 259 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR E 119 " pdb=" OH TYR I 33 " model vdw 2.267 3.040 nonbonded pdb=" O TRP I 117 " pdb=" OG1 THR I 120 " model vdw 2.268 3.040 nonbonded pdb=" O GLY B 131 " pdb=" OH TYR B 274 " model vdw 2.275 3.040 ... (remaining 164374 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 11 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 423 or (resid 424 and \ (name N or name CA or name C or name O or name CB )) or resid 425 through 510)) selection = (chain 'B' and (resid 11 through 84 or (resid 85 and (name N or name CA or name \ C or name O or name CB )) or resid 86 through 510)) } ncs_group { reference = (chain 'C' and (resid 974 through 1016 or (resid 1017 and (name N or name CA or \ name C or name O or name CB )) or resid 1018 through 1035)) selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.750 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 0.327 21728 Z= 0.332 Angle : 1.122 15.301 29402 Z= 0.590 Chirality : 0.063 0.375 3255 Planarity : 0.007 0.080 3796 Dihedral : 11.728 75.848 7957 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.35 % Allowed : 6.21 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 3.90 % Twisted General : 0.59 % 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: -4.82 (0.13), residues: 2606 helix: -2.69 (0.12), residues: 978 sheet: -2.70 (0.31), residues: 245 loop : -3.81 (0.14), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 182 TYR 0.034 0.003 TYR B 260 PHE 0.034 0.003 PHE G 415 TRP 0.026 0.002 TRP E 23 HIS 0.007 0.002 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00513 (21726) covalent geometry : angle 1.12209 (29402) hydrogen bonds : bond 0.14096 ( 730) hydrogen bonds : angle 7.25999 ( 2115) Misc. bond : bond 0.23464 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 518 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8032 (tt) cc_final: 0.7799 (tp) REVERT: A 98 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7304 (mtpp) REVERT: A 136 PHE cc_start: 0.8409 (t80) cc_final: 0.7964 (t80) REVERT: A 392 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: A 429 ASN cc_start: 0.7283 (m-40) cc_final: 0.6599 (p0) REVERT: A 484 ASP cc_start: 0.7962 (p0) cc_final: 0.7627 (p0) REVERT: B 139 THR cc_start: 0.8473 (p) cc_final: 0.8263 (p) REVERT: B 358 PHE cc_start: 0.7297 (p90) cc_final: 0.7055 (p90) REVERT: B 484 ASP cc_start: 0.7891 (p0) cc_final: 0.7569 (p0) REVERT: D 8 ILE cc_start: 0.8858 (pt) cc_final: 0.8619 (mm) REVERT: D 96 GLU cc_start: 0.8553 (tt0) cc_final: 0.8328 (tp30) REVERT: D 118 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8226 (tpp80) REVERT: D 123 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7027 (mp0) REVERT: D 135 GLN cc_start: 0.8472 (tt0) cc_final: 0.8042 (tp40) REVERT: D 137 TYR cc_start: 0.7536 (m-80) cc_final: 0.7072 (m-80) REVERT: D 164 VAL cc_start: 0.9014 (p) cc_final: 0.8712 (p) REVERT: E 8 ILE cc_start: 0.8924 (pt) cc_final: 0.8694 (mm) REVERT: E 118 ARG cc_start: 0.8705 (ttt90) cc_final: 0.8265 (tpp80) REVERT: E 123 GLU cc_start: 0.8960 (mm-30) cc_final: 0.7849 (mp0) REVERT: E 135 GLN cc_start: 0.8503 (tt0) cc_final: 0.8037 (tp40) REVERT: E 164 VAL cc_start: 0.9083 (p) cc_final: 0.8819 (p) REVERT: F 118 LEU cc_start: 0.9052 (tm) cc_final: 0.8738 (tp) REVERT: F 174 ARG cc_start: 0.7732 (ttt-90) cc_final: 0.7302 (ttt-90) REVERT: F 244 THR cc_start: 0.9435 (m) cc_final: 0.9199 (p) REVERT: F 343 ASP cc_start: 0.7651 (t70) cc_final: 0.7373 (t0) REVERT: G 118 LEU cc_start: 0.8989 (tm) cc_final: 0.8753 (tp) REVERT: G 244 THR cc_start: 0.9410 (m) cc_final: 0.9198 (p) REVERT: G 343 ASP cc_start: 0.7664 (t70) cc_final: 0.7406 (t0) REVERT: I 98 MET cc_start: 0.6998 (mtp) cc_final: 0.6763 (mtt) REVERT: I 100 MET cc_start: 0.8125 (mmm) cc_final: 0.7770 (mmt) REVERT: I 168 PHE cc_start: 0.8076 (m-10) cc_final: 0.7868 (m-10) REVERT: I 178 GLU cc_start: 0.8953 (pp20) cc_final: 0.8585 (pp20) outliers start: 8 outliers final: 2 residues processed: 525 average time/residue: 0.1668 time to fit residues: 130.1724 Evaluate side-chains 261 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 430 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0030 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 428 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN B 21 ASN B 428 ASN D 107 HIS E 107 HIS F 69 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN F 104 HIS ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 GLN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 HIS G 221 ASN ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN I 140 GLN I 258 HIS I 313 HIS C1000 ASN H1000 ASN H1018 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.109125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.085669 restraints weight = 72113.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.086947 restraints weight = 47378.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.087538 restraints weight = 36662.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088447 restraints weight = 32250.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088402 restraints weight = 29777.072| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21728 Z= 0.166 Angle : 0.797 10.367 29402 Z= 0.416 Chirality : 0.049 0.266 3255 Planarity : 0.005 0.072 3796 Dihedral : 7.601 47.956 2851 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 3.24 % Allowed : 11.30 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 1.30 % Twisted General : 0.31 % 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: -3.87 (0.14), residues: 2606 helix: -1.19 (0.15), residues: 1031 sheet: -2.76 (0.31), residues: 245 loop : -3.81 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 68 TYR 0.018 0.002 TYR A 260 PHE 0.024 0.002 PHE I 225 TRP 0.016 0.002 TRP I 134 HIS 0.005 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00360 (21726) covalent geometry : angle 0.79651 (29402) hydrogen bonds : bond 0.04200 ( 730) hydrogen bonds : angle 5.52438 ( 2115) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 294 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: A 415 PHE cc_start: 0.8060 (t80) cc_final: 0.7818 (t80) REVERT: A 484 ASP cc_start: 0.8292 (p0) cc_final: 0.7926 (p0) REVERT: B 184 LEU cc_start: 0.7797 (tt) cc_final: 0.7433 (tt) REVERT: B 391 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8011 (tp) REVERT: B 392 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7313 (m-10) REVERT: B 425 GLU cc_start: 0.6425 (tt0) cc_final: 0.6160 (tm-30) REVERT: B 484 ASP cc_start: 0.8277 (p0) cc_final: 0.7967 (p0) REVERT: D 118 ARG cc_start: 0.8897 (ttt90) cc_final: 0.8384 (tpp80) REVERT: D 123 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7218 (mp0) REVERT: D 136 ASN cc_start: 0.7777 (p0) cc_final: 0.7515 (p0) REVERT: D 137 TYR cc_start: 0.7970 (m-80) cc_final: 0.7481 (m-80) REVERT: E 118 ARG cc_start: 0.8910 (ttt90) cc_final: 0.8414 (tpp80) REVERT: E 123 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7873 (mp0) REVERT: E 137 TYR cc_start: 0.7682 (m-80) cc_final: 0.7469 (m-80) REVERT: E 161 PHE cc_start: 0.8527 (m-80) cc_final: 0.8322 (m-80) REVERT: F 256 VAL cc_start: 0.9562 (t) cc_final: 0.9278 (p) REVERT: F 264 ASP cc_start: 0.8625 (t0) cc_final: 0.8388 (t70) REVERT: F 343 ASP cc_start: 0.8176 (t70) cc_final: 0.7728 (t0) REVERT: G 256 VAL cc_start: 0.9566 (t) cc_final: 0.9281 (p) REVERT: G 343 ASP cc_start: 0.8183 (t70) cc_final: 0.7735 (t0) REVERT: I 66 ILE cc_start: -0.3706 (OUTLIER) cc_final: -0.4031 (tt) REVERT: I 98 MET cc_start: 0.7205 (mtp) cc_final: 0.6880 (mtp) REVERT: I 100 MET cc_start: 0.7802 (mmm) cc_final: 0.7071 (tpp) REVERT: I 134 TRP cc_start: 0.7074 (m-90) cc_final: 0.6781 (m-90) REVERT: I 178 GLU cc_start: 0.9094 (pp20) cc_final: 0.8721 (pp20) REVERT: I 189 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7388 (t80) REVERT: I 193 LEU cc_start: 0.9359 (tt) cc_final: 0.9128 (tt) REVERT: I 263 LEU cc_start: 0.3770 (OUTLIER) cc_final: 0.3324 (pp) REVERT: H 1018 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7997 (pm20) outliers start: 75 outliers final: 35 residues processed: 346 average time/residue: 0.1680 time to fit residues: 85.6715 Evaluate side-chains 264 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 259 optimal weight: 2.9990 chunk 136 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 123 optimal weight: 0.0000 chunk 181 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 256 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 overall best weight: 0.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN I 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.110444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086564 restraints weight = 72801.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088185 restraints weight = 47014.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088775 restraints weight = 35705.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088983 restraints weight = 31815.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089086 restraints weight = 30144.866| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21728 Z= 0.132 Angle : 0.755 10.040 29402 Z= 0.387 Chirality : 0.048 0.314 3255 Planarity : 0.005 0.061 3796 Dihedral : 6.904 38.389 2849 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.24 % Allowed : 12.77 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.41 (0.15), residues: 2606 helix: -0.60 (0.16), residues: 1035 sheet: -2.64 (0.31), residues: 245 loop : -3.73 (0.14), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 218 TYR 0.022 0.001 TYR A 274 PHE 0.022 0.001 PHE H1021 TRP 0.026 0.001 TRP B 17 HIS 0.006 0.001 HIS I 303 Details of bonding type rmsd covalent geometry : bond 0.00286 (21726) covalent geometry : angle 0.75476 (29402) hydrogen bonds : bond 0.03597 ( 730) hydrogen bonds : angle 5.13884 ( 2115) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 274 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8106 (pt0) REVERT: A 392 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7650 (m-10) REVERT: A 484 ASP cc_start: 0.8290 (p0) cc_final: 0.7880 (p0) REVERT: A 503 ARG cc_start: 0.8951 (ptp-170) cc_final: 0.8711 (ptp90) REVERT: B 153 ARG cc_start: 0.5545 (ttp-170) cc_final: 0.5335 (ttp-170) REVERT: B 287 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: B 392 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: B 425 GLU cc_start: 0.6326 (tt0) cc_final: 0.5989 (tm-30) REVERT: B 484 ASP cc_start: 0.8329 (p0) cc_final: 0.8012 (p0) REVERT: D 118 ARG cc_start: 0.8892 (ttt90) cc_final: 0.8373 (tpp80) REVERT: D 123 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7292 (mp0) REVERT: D 136 ASN cc_start: 0.7731 (p0) cc_final: 0.7498 (p0) REVERT: D 137 TYR cc_start: 0.7756 (m-80) cc_final: 0.7377 (m-80) REVERT: E 118 ARG cc_start: 0.8894 (ttt90) cc_final: 0.8406 (tpp80) REVERT: E 123 GLU cc_start: 0.8688 (mm-30) cc_final: 0.7861 (mp0) REVERT: E 161 PHE cc_start: 0.8484 (m-80) cc_final: 0.8187 (m-80) REVERT: F 256 VAL cc_start: 0.9586 (t) cc_final: 0.9327 (p) REVERT: F 343 ASP cc_start: 0.8105 (t70) cc_final: 0.7667 (t0) REVERT: F 362 GLU cc_start: 0.8058 (pm20) cc_final: 0.7474 (pm20) REVERT: G 256 VAL cc_start: 0.9599 (t) cc_final: 0.9348 (p) REVERT: G 343 ASP cc_start: 0.8116 (t70) cc_final: 0.7696 (t0) REVERT: G 362 GLU cc_start: 0.8024 (pm20) cc_final: 0.7424 (pm20) REVERT: I 66 ILE cc_start: -0.3516 (OUTLIER) cc_final: -0.3790 (tt) REVERT: I 100 MET cc_start: 0.7761 (mmm) cc_final: 0.7135 (tmm) REVERT: I 134 TRP cc_start: 0.7144 (m-90) cc_final: 0.6788 (m-90) REVERT: I 178 GLU cc_start: 0.9083 (pp20) cc_final: 0.8745 (pp20) REVERT: I 189 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7357 (t80) REVERT: I 193 LEU cc_start: 0.9342 (tt) cc_final: 0.9104 (tt) REVERT: I 263 LEU cc_start: 0.4140 (OUTLIER) cc_final: 0.3736 (pp) REVERT: H 1018 GLN cc_start: 0.8236 (mt0) cc_final: 0.7930 (pm20) outliers start: 75 outliers final: 31 residues processed: 327 average time/residue: 0.1518 time to fit residues: 75.1437 Evaluate side-chains 278 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 245 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 25 optimal weight: 0.0770 chunk 175 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS D 136 ASN E 100 HIS ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN F 295 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 ASN G 46 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 421 ASN C 975 ASN H1018 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.101764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078162 restraints weight = 75254.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078859 restraints weight = 54005.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079802 restraints weight = 42413.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080551 restraints weight = 37759.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080637 restraints weight = 35820.863| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 21728 Z= 0.412 Angle : 0.994 14.893 29402 Z= 0.518 Chirality : 0.055 0.291 3255 Planarity : 0.006 0.082 3796 Dihedral : 7.572 40.218 2847 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.58 % Favored : 84.42 % Rotamer: Outliers : 4.62 % Allowed : 14.54 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.54 (0.15), residues: 2606 helix: -0.76 (0.15), residues: 1057 sheet: -2.81 (0.29), residues: 260 loop : -3.78 (0.14), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 24 TYR 0.028 0.003 TYR A 35 PHE 0.029 0.003 PHE A 358 TRP 0.059 0.003 TRP A 17 HIS 0.035 0.003 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00889 (21726) covalent geometry : angle 0.99351 (29402) hydrogen bonds : bond 0.04702 ( 730) hydrogen bonds : angle 5.83247 ( 2115) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 218 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ASN cc_start: 0.7320 (m-40) cc_final: 0.6137 (p0) REVERT: B 274 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7026 (t80) REVERT: B 425 GLU cc_start: 0.6820 (tt0) cc_final: 0.6401 (tm-30) REVERT: B 446 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8058 (mmmm) REVERT: D 123 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7735 (mp0) REVERT: D 136 ASN cc_start: 0.7817 (p0) cc_final: 0.7387 (p0) REVERT: D 137 TYR cc_start: 0.8217 (m-80) cc_final: 0.7890 (m-80) REVERT: E 68 ARG cc_start: 0.8203 (tmm-80) cc_final: 0.7970 (tmm-80) REVERT: E 123 GLU cc_start: 0.8816 (mm-30) cc_final: 0.7955 (mp0) REVERT: F 343 ASP cc_start: 0.8347 (t70) cc_final: 0.7832 (t0) REVERT: G 343 ASP cc_start: 0.8333 (t70) cc_final: 0.7827 (t0) REVERT: I 66 ILE cc_start: -0.3221 (OUTLIER) cc_final: -0.3540 (tt) REVERT: I 100 MET cc_start: 0.7806 (mmm) cc_final: 0.7024 (tmm) REVERT: I 134 TRP cc_start: 0.7246 (m-90) cc_final: 0.6906 (m-90) REVERT: I 168 PHE cc_start: 0.8687 (m-80) cc_final: 0.8384 (m-80) REVERT: I 189 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7334 (t80) REVERT: H 995 ASN cc_start: 0.5280 (m110) cc_final: 0.5075 (t0) outliers start: 107 outliers final: 65 residues processed: 297 average time/residue: 0.1554 time to fit residues: 68.9494 Evaluate side-chains 251 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain H residue 1028 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 55 optimal weight: 0.2980 chunk 217 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN F 120 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 ASN G 120 ASN ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 421 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.106757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083536 restraints weight = 72920.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.084837 restraints weight = 48733.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085701 restraints weight = 38016.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.085681 restraints weight = 32675.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.085925 restraints weight = 31084.935| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21728 Z= 0.136 Angle : 0.752 10.778 29402 Z= 0.388 Chirality : 0.048 0.256 3255 Planarity : 0.004 0.055 3796 Dihedral : 6.812 38.595 2845 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 3.02 % Allowed : 15.40 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.09 (0.15), residues: 2606 helix: -0.20 (0.16), residues: 1040 sheet: -2.62 (0.31), residues: 239 loop : -3.65 (0.14), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 324 TYR 0.021 0.001 TYR A 274 PHE 0.033 0.002 PHE B 358 TRP 0.046 0.002 TRP A 17 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00298 (21726) covalent geometry : angle 0.75180 (29402) hydrogen bonds : bond 0.03517 ( 730) hydrogen bonds : angle 5.09840 ( 2115) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 239 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7780 (tt) cc_final: 0.7411 (tt) REVERT: A 260 TYR cc_start: 0.8742 (t80) cc_final: 0.8396 (t80) REVERT: B 184 LEU cc_start: 0.7872 (tt) cc_final: 0.7663 (tt) REVERT: B 260 TYR cc_start: 0.8781 (t80) cc_final: 0.8417 (t80) REVERT: B 392 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: B 425 GLU cc_start: 0.6779 (tt0) cc_final: 0.6565 (tm-30) REVERT: D 118 ARG cc_start: 0.8855 (ttt90) cc_final: 0.8492 (tpp80) REVERT: D 123 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7759 (mp0) REVERT: D 136 ASN cc_start: 0.7717 (p0) cc_final: 0.7315 (p0) REVERT: D 137 TYR cc_start: 0.8033 (m-80) cc_final: 0.7751 (m-80) REVERT: E 68 ARG cc_start: 0.8166 (tmm-80) cc_final: 0.7823 (tmm-80) REVERT: E 118 ARG cc_start: 0.8866 (ttt90) cc_final: 0.8499 (tpp80) REVERT: E 123 GLU cc_start: 0.8753 (mm-30) cc_final: 0.7909 (mp0) REVERT: F 267 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6946 (mm-40) REVERT: F 343 ASP cc_start: 0.8356 (t70) cc_final: 0.7987 (t0) REVERT: F 362 GLU cc_start: 0.8136 (pm20) cc_final: 0.7726 (pm20) REVERT: G 343 ASP cc_start: 0.8336 (t70) cc_final: 0.7975 (t0) REVERT: G 362 GLU cc_start: 0.8135 (pm20) cc_final: 0.7737 (pm20) REVERT: I 66 ILE cc_start: -0.3691 (OUTLIER) cc_final: -0.3967 (tt) REVERT: I 98 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.5147 (ptp) REVERT: I 100 MET cc_start: 0.7696 (mmm) cc_final: 0.7156 (tmm) REVERT: I 134 TRP cc_start: 0.7223 (m-90) cc_final: 0.6994 (m-90) REVERT: I 168 PHE cc_start: 0.8632 (m-80) cc_final: 0.8369 (m-80) outliers start: 70 outliers final: 50 residues processed: 289 average time/residue: 0.1579 time to fit residues: 68.3101 Evaluate side-chains 261 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 301 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 223 optimal weight: 0.0010 chunk 13 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 chunk 210 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.107614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.084573 restraints weight = 73093.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085618 restraints weight = 50923.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086342 restraints weight = 38872.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.086918 restraints weight = 34676.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086976 restraints weight = 32324.216| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 21728 Z= 0.135 Angle : 0.732 13.170 29402 Z= 0.374 Chirality : 0.047 0.244 3255 Planarity : 0.004 0.052 3796 Dihedral : 6.373 39.479 2845 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.12 % Favored : 86.88 % Rotamer: Outliers : 3.45 % Allowed : 15.92 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.82 (0.16), residues: 2606 helix: 0.05 (0.16), residues: 1041 sheet: -2.41 (0.32), residues: 239 loop : -3.55 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 14 TYR 0.014 0.001 TYR A 274 PHE 0.030 0.001 PHE B 358 TRP 0.046 0.002 TRP B 17 HIS 0.003 0.001 HIS I 64 Details of bonding type rmsd covalent geometry : bond 0.00303 (21726) covalent geometry : angle 0.73204 (29402) hydrogen bonds : bond 0.03305 ( 730) hydrogen bonds : angle 4.83988 ( 2115) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 252 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.7726 (m100) REVERT: A 260 TYR cc_start: 0.8701 (t80) cc_final: 0.8433 (t80) REVERT: A 503 ARG cc_start: 0.8983 (ptp-170) cc_final: 0.8779 (ptp90) REVERT: B 33 LYS cc_start: 0.7605 (mptt) cc_final: 0.7291 (mmtm) REVERT: B 184 LEU cc_start: 0.7656 (tt) cc_final: 0.7324 (mt) REVERT: B 260 TYR cc_start: 0.8724 (t80) cc_final: 0.8474 (t80) REVERT: B 332 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7740 (mmtt) REVERT: B 392 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: B 446 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8596 (mmmm) REVERT: D 118 ARG cc_start: 0.8910 (ttt90) cc_final: 0.8550 (tpp80) REVERT: D 123 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7645 (mp0) REVERT: D 136 ASN cc_start: 0.7778 (p0) cc_final: 0.7428 (p0) REVERT: E 46 TYR cc_start: 0.8434 (p90) cc_final: 0.8101 (p90) REVERT: E 68 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.8018 (tmm-80) REVERT: E 118 ARG cc_start: 0.8889 (ttt90) cc_final: 0.8511 (tpp80) REVERT: E 123 GLU cc_start: 0.8753 (mm-30) cc_final: 0.7869 (mp0) REVERT: F 267 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7038 (mm-40) REVERT: F 343 ASP cc_start: 0.8314 (t70) cc_final: 0.7995 (t0) REVERT: F 362 GLU cc_start: 0.8066 (pm20) cc_final: 0.7484 (pm20) REVERT: G 343 ASP cc_start: 0.8277 (t70) cc_final: 0.7961 (t0) REVERT: G 362 GLU cc_start: 0.8006 (pm20) cc_final: 0.7397 (pm20) REVERT: I 66 ILE cc_start: -0.3057 (OUTLIER) cc_final: -0.3342 (tt) REVERT: I 100 MET cc_start: 0.7623 (mmm) cc_final: 0.6860 (tmm) REVERT: I 134 TRP cc_start: 0.7173 (m-90) cc_final: 0.6616 (m-90) REVERT: I 168 PHE cc_start: 0.8647 (m-80) cc_final: 0.8397 (m-80) REVERT: I 189 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7194 (t80) REVERT: I 239 MET cc_start: 0.6113 (mtt) cc_final: 0.5721 (mmm) REVERT: I 278 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5681 (pp) REVERT: I 279 ASP cc_start: 0.5864 (m-30) cc_final: 0.5440 (p0) REVERT: I 346 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7801 (mp) REVERT: H 995 ASN cc_start: 0.5785 (m110) cc_final: 0.5426 (t0) outliers start: 80 outliers final: 48 residues processed: 313 average time/residue: 0.1493 time to fit residues: 70.3546 Evaluate side-chains 275 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain C residue 1022 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 172 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 39 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 HIS ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.108068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.084995 restraints weight = 73056.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086041 restraints weight = 47618.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087104 restraints weight = 36745.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.087192 restraints weight = 32555.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.087241 restraints weight = 30861.396| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21728 Z= 0.127 Angle : 0.729 12.115 29402 Z= 0.372 Chirality : 0.047 0.241 3255 Planarity : 0.004 0.058 3796 Dihedral : 6.182 38.132 2845 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 3.36 % Allowed : 16.31 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.69 (0.16), residues: 2606 helix: 0.13 (0.16), residues: 1052 sheet: -2.35 (0.32), residues: 243 loop : -3.47 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 981 TYR 0.025 0.001 TYR D 46 PHE 0.026 0.001 PHE A 358 TRP 0.046 0.002 TRP A 17 HIS 0.008 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00282 (21726) covalent geometry : angle 0.72939 (29402) hydrogen bonds : bond 0.03197 ( 730) hydrogen bonds : angle 4.71803 ( 2115) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.7968 (OUTLIER) cc_final: 0.7703 (m100) REVERT: A 33 LYS cc_start: 0.7972 (mptt) cc_final: 0.7667 (mmtm) REVERT: A 260 TYR cc_start: 0.8680 (t80) cc_final: 0.8400 (t80) REVERT: B 17 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.7819 (m100) REVERT: B 33 LYS cc_start: 0.7798 (mptt) cc_final: 0.7470 (mmtm) REVERT: B 220 VAL cc_start: 0.7910 (t) cc_final: 0.7599 (m) REVERT: B 260 TYR cc_start: 0.8772 (t80) cc_final: 0.8546 (t80) REVERT: B 392 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: D 6 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9070 (p) REVERT: D 118 ARG cc_start: 0.8893 (ttt90) cc_final: 0.8547 (tpp80) REVERT: D 123 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7643 (mp0) REVERT: E 46 TYR cc_start: 0.8378 (p90) cc_final: 0.8010 (p90) REVERT: E 113 MET cc_start: 0.7943 (mmm) cc_final: 0.7627 (mmm) REVERT: E 118 ARG cc_start: 0.8893 (ttt90) cc_final: 0.8510 (tpp80) REVERT: E 123 GLU cc_start: 0.8760 (mm-30) cc_final: 0.7777 (mp0) REVERT: F 267 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7001 (mm-40) REVERT: F 343 ASP cc_start: 0.8199 (t70) cc_final: 0.7854 (t0) REVERT: F 362 GLU cc_start: 0.8000 (pm20) cc_final: 0.7434 (pm20) REVERT: G 343 ASP cc_start: 0.8170 (t70) cc_final: 0.7825 (t0) REVERT: G 362 GLU cc_start: 0.7929 (pm20) cc_final: 0.7327 (pm20) REVERT: I 66 ILE cc_start: -0.3099 (OUTLIER) cc_final: -0.3383 (tt) REVERT: I 100 MET cc_start: 0.7638 (mmm) cc_final: 0.6848 (tmm) REVERT: I 134 TRP cc_start: 0.7187 (m-90) cc_final: 0.6577 (m-90) REVERT: I 168 PHE cc_start: 0.8635 (m-80) cc_final: 0.8361 (m-80) REVERT: I 189 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7214 (t80) REVERT: I 279 ASP cc_start: 0.5744 (m-30) cc_final: 0.5484 (p0) outliers start: 78 outliers final: 48 residues processed: 293 average time/residue: 0.1550 time to fit residues: 67.9617 Evaluate side-chains 272 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain C residue 1022 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 175 optimal weight: 7.9990 chunk 76 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 84 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 125 optimal weight: 0.0770 chunk 135 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083074 restraints weight = 73232.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.084111 restraints weight = 48715.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084909 restraints weight = 38061.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.084920 restraints weight = 35193.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.085029 restraints weight = 33165.544| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21728 Z= 0.180 Angle : 0.769 11.554 29402 Z= 0.392 Chirality : 0.048 0.239 3255 Planarity : 0.004 0.053 3796 Dihedral : 6.267 38.407 2845 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 3.49 % Allowed : 16.39 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.66 (0.16), residues: 2606 helix: 0.15 (0.16), residues: 1056 sheet: -2.34 (0.33), residues: 243 loop : -3.46 (0.15), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 241 TYR 0.021 0.001 TYR D 46 PHE 0.024 0.002 PHE B 358 TRP 0.046 0.002 TRP B 17 HIS 0.004 0.001 HIS I 64 Details of bonding type rmsd covalent geometry : bond 0.00398 (21726) covalent geometry : angle 0.76902 (29402) hydrogen bonds : bond 0.03380 ( 730) hydrogen bonds : angle 4.85610 ( 2115) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 222 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.7724 (m100) REVERT: A 33 LYS cc_start: 0.7642 (mptt) cc_final: 0.7343 (mmtp) REVERT: A 181 TYR cc_start: 0.7976 (t80) cc_final: 0.7750 (t80) REVERT: A 387 LEU cc_start: 0.9479 (mm) cc_final: 0.9259 (mt) REVERT: B 33 LYS cc_start: 0.7896 (mptt) cc_final: 0.7096 (mmtp) REVERT: B 181 TYR cc_start: 0.8010 (t80) cc_final: 0.7805 (t80) REVERT: B 220 VAL cc_start: 0.8011 (t) cc_final: 0.7693 (m) REVERT: B 274 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6372 (t80) REVERT: B 392 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7558 (m-10) REVERT: D 118 ARG cc_start: 0.8898 (ttt90) cc_final: 0.8564 (tpp80) REVERT: D 123 GLU cc_start: 0.8722 (mm-30) cc_final: 0.7785 (mp0) REVERT: E 46 TYR cc_start: 0.8335 (p90) cc_final: 0.8025 (p90) REVERT: E 118 ARG cc_start: 0.8924 (ttt90) cc_final: 0.8564 (tpp80) REVERT: E 123 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7902 (mp0) REVERT: F 267 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7167 (mm-40) REVERT: F 343 ASP cc_start: 0.8291 (t70) cc_final: 0.7964 (t0) REVERT: F 362 GLU cc_start: 0.8108 (pm20) cc_final: 0.7479 (pm20) REVERT: G 343 ASP cc_start: 0.8264 (t70) cc_final: 0.7948 (t0) REVERT: G 362 GLU cc_start: 0.7956 (pm20) cc_final: 0.7733 (pm20) REVERT: I 66 ILE cc_start: -0.2995 (OUTLIER) cc_final: -0.3556 (tp) REVERT: I 100 MET cc_start: 0.7816 (mmm) cc_final: 0.6968 (tmm) REVERT: I 134 TRP cc_start: 0.7246 (m-90) cc_final: 0.6628 (m-90) REVERT: I 279 ASP cc_start: 0.6005 (m-30) cc_final: 0.5621 (p0) REVERT: C 981 ARG cc_start: 0.6252 (mtt180) cc_final: 0.5974 (mtt-85) REVERT: H 995 ASN cc_start: 0.5835 (m110) cc_final: 0.5523 (t0) outliers start: 81 outliers final: 56 residues processed: 283 average time/residue: 0.1564 time to fit residues: 66.9894 Evaluate side-chains 268 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain C residue 1022 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 167 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN G 387 ASN ** G 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1012 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.107274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084187 restraints weight = 73529.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085318 restraints weight = 50231.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.086180 restraints weight = 39430.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.086370 restraints weight = 34144.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.086556 restraints weight = 32517.574| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21728 Z= 0.147 Angle : 0.753 12.744 29402 Z= 0.382 Chirality : 0.047 0.259 3255 Planarity : 0.004 0.052 3796 Dihedral : 6.184 38.010 2845 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 3.28 % Allowed : 16.78 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.60 (0.16), residues: 2606 helix: 0.19 (0.16), residues: 1052 sheet: -2.31 (0.33), residues: 243 loop : -3.40 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 324 TYR 0.026 0.001 TYR A 84 PHE 0.022 0.001 PHE C1021 TRP 0.046 0.002 TRP A 17 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00326 (21726) covalent geometry : angle 0.75273 (29402) hydrogen bonds : bond 0.03219 ( 730) hydrogen bonds : angle 4.77251 ( 2115) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.7675 (m100) REVERT: A 33 LYS cc_start: 0.7973 (mptt) cc_final: 0.7265 (mmtp) REVERT: A 262 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8965 (pp) REVERT: A 387 LEU cc_start: 0.9468 (mm) cc_final: 0.9238 (mt) REVERT: B 33 LYS cc_start: 0.7961 (mptt) cc_final: 0.7267 (mmtp) REVERT: B 181 TYR cc_start: 0.7994 (t80) cc_final: 0.7757 (t80) REVERT: B 220 VAL cc_start: 0.7922 (t) cc_final: 0.7640 (m) REVERT: B 262 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8958 (pp) REVERT: B 274 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.5926 (t80) REVERT: B 392 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: D 6 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9047 (p) REVERT: D 113 MET cc_start: 0.7926 (mmm) cc_final: 0.7692 (mmm) REVERT: D 118 ARG cc_start: 0.8919 (ttt90) cc_final: 0.8566 (tpp80) REVERT: D 123 GLU cc_start: 0.8689 (mm-30) cc_final: 0.7653 (mp0) REVERT: E 118 ARG cc_start: 0.8945 (ttt90) cc_final: 0.8587 (tpp80) REVERT: E 123 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7908 (mp0) REVERT: F 267 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7061 (mm-40) REVERT: F 343 ASP cc_start: 0.8194 (t70) cc_final: 0.7820 (t0) REVERT: F 362 GLU cc_start: 0.8039 (pm20) cc_final: 0.7781 (pm20) REVERT: G 343 ASP cc_start: 0.8182 (t70) cc_final: 0.7828 (t0) REVERT: G 362 GLU cc_start: 0.7953 (pm20) cc_final: 0.7667 (pm20) REVERT: I 66 ILE cc_start: -0.3006 (OUTLIER) cc_final: -0.3564 (tp) REVERT: I 100 MET cc_start: 0.7827 (mmm) cc_final: 0.6978 (tmm) REVERT: I 134 TRP cc_start: 0.7195 (m-90) cc_final: 0.6535 (m-90) REVERT: I 279 ASP cc_start: 0.6091 (m-30) cc_final: 0.5695 (p0) REVERT: I 280 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7980 (mmmt) REVERT: C 981 ARG cc_start: 0.6279 (mtt180) cc_final: 0.5986 (mtt-85) REVERT: H 981 ARG cc_start: 0.6217 (mtt180) cc_final: 0.6014 (mtt-85) outliers start: 76 outliers final: 49 residues processed: 278 average time/residue: 0.1587 time to fit residues: 66.3458 Evaluate side-chains 273 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain C residue 1022 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 243 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 178 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.106208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082871 restraints weight = 73572.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.084022 restraints weight = 50475.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084759 restraints weight = 38675.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085472 restraints weight = 34872.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.085657 restraints weight = 32134.227| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21728 Z= 0.174 Angle : 0.768 10.130 29402 Z= 0.392 Chirality : 0.049 0.474 3255 Planarity : 0.004 0.052 3796 Dihedral : 6.231 38.301 2845 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 2.93 % Allowed : 17.21 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.67 (0.16), residues: 2606 helix: 0.12 (0.16), residues: 1071 sheet: -2.33 (0.33), residues: 243 loop : -3.49 (0.15), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 324 TYR 0.043 0.001 TYR E 46 PHE 0.023 0.002 PHE B 358 TRP 0.045 0.002 TRP A 17 HIS 0.007 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00387 (21726) covalent geometry : angle 0.76767 (29402) hydrogen bonds : bond 0.03331 ( 730) hydrogen bonds : angle 4.83834 ( 2115) Misc. bond : bond 0.00032 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.7616 (m100) REVERT: A 33 LYS cc_start: 0.7711 (mptt) cc_final: 0.7424 (mmtp) REVERT: A 387 LEU cc_start: 0.9503 (mm) cc_final: 0.9266 (mt) REVERT: B 33 LYS cc_start: 0.7955 (mptt) cc_final: 0.7393 (mmtp) REVERT: B 181 TYR cc_start: 0.8053 (t80) cc_final: 0.7794 (t80) REVERT: B 220 VAL cc_start: 0.8064 (t) cc_final: 0.7758 (m) REVERT: B 262 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8949 (pp) REVERT: B 274 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6097 (t80) REVERT: B 392 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: D 6 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.8947 (p) REVERT: D 118 ARG cc_start: 0.8926 (ttt90) cc_final: 0.8589 (tpp80) REVERT: D 123 GLU cc_start: 0.8745 (mm-30) cc_final: 0.7827 (mp0) REVERT: E 118 ARG cc_start: 0.8952 (ttt90) cc_final: 0.8594 (tpp80) REVERT: E 123 GLU cc_start: 0.8766 (mm-30) cc_final: 0.7915 (mp0) REVERT: F 267 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7129 (mm-40) REVERT: F 343 ASP cc_start: 0.8267 (t70) cc_final: 0.7691 (t0) REVERT: F 362 GLU cc_start: 0.8079 (pm20) cc_final: 0.7812 (pm20) REVERT: F 390 MET cc_start: 0.7485 (ttp) cc_final: 0.7240 (mtp) REVERT: G 343 ASP cc_start: 0.8260 (t70) cc_final: 0.7692 (t0) REVERT: G 362 GLU cc_start: 0.7842 (pm20) cc_final: 0.7621 (pm20) REVERT: I 66 ILE cc_start: -0.2958 (OUTLIER) cc_final: -0.3518 (tp) REVERT: I 100 MET cc_start: 0.7849 (mmm) cc_final: 0.7003 (tmm) REVERT: I 134 TRP cc_start: 0.7223 (m-90) cc_final: 0.7018 (m-90) REVERT: I 189 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7093 (t80) REVERT: I 279 ASP cc_start: 0.6183 (m-30) cc_final: 0.5750 (p0) REVERT: C 981 ARG cc_start: 0.6285 (mtt180) cc_final: 0.6005 (mtt-85) REVERT: H 981 ARG cc_start: 0.6397 (mtt180) cc_final: 0.6158 (mtt-85) outliers start: 68 outliers final: 54 residues processed: 263 average time/residue: 0.1503 time to fit residues: 59.0042 Evaluate side-chains 264 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain C residue 1022 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 93 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 74 optimal weight: 0.0980 chunk 167 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 257 optimal weight: 0.0370 chunk 158 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.108452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085785 restraints weight = 73236.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086861 restraints weight = 49002.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087681 restraints weight = 38167.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.087778 restraints weight = 34549.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088027 restraints weight = 32950.113| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21728 Z= 0.127 Angle : 0.745 9.762 29402 Z= 0.378 Chirality : 0.048 0.460 3255 Planarity : 0.004 0.054 3796 Dihedral : 5.986 37.621 2845 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.29 % Allowed : 17.82 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.50 (0.16), residues: 2606 helix: 0.27 (0.16), residues: 1059 sheet: -2.20 (0.33), residues: 243 loop : -3.38 (0.15), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 324 TYR 0.030 0.001 TYR D 46 PHE 0.025 0.001 PHE A 358 TRP 0.046 0.001 TRP A 17 HIS 0.004 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00280 (21726) covalent geometry : angle 0.74484 (29402) hydrogen bonds : bond 0.03105 ( 730) hydrogen bonds : angle 4.64701 ( 2115) Misc. bond : bond 0.00031 ( 2) =============================================================================== Job complete usr+sys time: 3301.00 seconds wall clock time: 57 minutes 59.41 seconds (3479.41 seconds total)