Starting phenix.real_space_refine on Tue Jul 29 09:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1n_8958/07_2025/6e1n_8958_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1n_8958/07_2025/6e1n_8958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e1n_8958/07_2025/6e1n_8958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1n_8958/07_2025/6e1n_8958.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1n_8958/07_2025/6e1n_8958_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1n_8958/07_2025/6e1n_8958_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 36 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 8 5.49 5 S 46 5.16 5 C 7164 2.51 5 N 1576 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10682 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5145 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 18, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' CA': 3, '3PH': 1, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.94, per 1000 atoms: 0.65 Number of scatterers: 10682 At special positions: 0 Unit cell: (137.363, 91.17, 106.973, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 46 16.00 P 8 15.00 O 1882 8.00 N 1576 7.00 C 7164 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.624A pdb=" N PHE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.626A pdb=" N PHE A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.839A pdb=" N PHE A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.533A pdb=" N TRP A 92 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 136 removed outlier: 3.830A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 150 through 173 removed outlier: 3.512A pdb=" N VAL A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 163 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 4.067A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.923A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 238 removed outlier: 4.161A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.911A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.967A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.663A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.625A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 3.630A pdb=" N LEU A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.896A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 removed outlier: 5.370A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 4.172A pdb=" N ASP A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.690A pdb=" N LEU A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.622A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.977A pdb=" N THR A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 487 removed outlier: 3.723A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 Processing helix chain 'A' and resid 496 through 513 removed outlier: 3.616A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 534 through 539 removed outlier: 4.281A pdb=" N MET A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 551 through 565 removed outlier: 3.696A pdb=" N ILE A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 567 through 587 removed outlier: 4.028A pdb=" N ILE A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.668A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.812A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.960A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 688 removed outlier: 3.545A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.564A pdb=" N PHE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.719A pdb=" N PHE B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 78 through 87 removed outlier: 4.705A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.534A pdb=" N TRP B 92 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 136 removed outlier: 3.823A pdb=" N ILE B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 150 through 173 removed outlier: 3.959A pdb=" N LYS B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 163 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 4.044A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 193 " --> pdb=" O TYR B 189 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.927A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 238 removed outlier: 4.205A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.901A pdb=" N LEU B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.981A pdb=" N GLN B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.666A pdb=" N VAL B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.567A pdb=" N LEU B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 333 removed outlier: 3.654A pdb=" N LEU B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 355 removed outlier: 4.060A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 removed outlier: 5.159A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 4.151A pdb=" N LEU B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.714A pdb=" N LEU B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 456 removed outlier: 3.909A pdb=" N THR B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 487 removed outlier: 3.751A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 477 " --> pdb=" O TRP B 473 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 493 Processing helix chain 'B' and resid 496 through 513 removed outlier: 3.692A pdb=" N LEU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 534 through 539 removed outlier: 4.223A pdb=" N MET B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.616A pdb=" N ILE B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 567 through 587 removed outlier: 4.095A pdb=" N ILE B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 616 through 629 removed outlier: 3.644A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.778A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 663 removed outlier: 3.974A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 688 removed outlier: 3.557A pdb=" N LEU B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1470 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: 2.86 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1657 1.31 - 1.43: 3084 1.43 - 1.56: 6077 1.56 - 1.68: 32 1.68 - 1.81: 74 Bond restraints: 10924 Sorted by residual: bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C31 3PH A 812 " pdb=" O31 3PH A 812 " ideal model delta sigma weight residual 1.325 1.409 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 13485 2.49 - 4.98: 1060 4.98 - 7.46: 147 7.46 - 9.95: 61 9.95 - 12.44: 11 Bond angle restraints: 14764 Sorted by residual: angle pdb=" C ILE A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta sigma weight residual 121.19 130.14 -8.95 1.59e+00 3.96e-01 3.17e+01 angle pdb=" C ILE B 371 " pdb=" N PHE B 372 " pdb=" CA PHE B 372 " ideal model delta sigma weight residual 121.19 130.12 -8.93 1.59e+00 3.96e-01 3.15e+01 angle pdb=" C THR B 264 " pdb=" CA THR B 264 " pdb=" CB THR B 264 " ideal model delta sigma weight residual 111.80 104.25 7.55 1.46e+00 4.69e-01 2.67e+01 angle pdb=" C THR A 264 " pdb=" CA THR A 264 " pdb=" CB THR A 264 " ideal model delta sigma weight residual 111.80 104.38 7.42 1.46e+00 4.69e-01 2.58e+01 angle pdb=" C VAL A 628 " pdb=" N MET A 629 " pdb=" CA MET A 629 " ideal model delta sigma weight residual 122.35 129.25 -6.90 1.46e+00 4.69e-01 2.23e+01 ... (remaining 14759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5733 17.40 - 34.80: 485 34.80 - 52.20: 118 52.20 - 69.61: 42 69.61 - 87.01: 6 Dihedral angle restraints: 6384 sinusoidal: 2608 harmonic: 3776 Sorted by residual: dihedral pdb=" CA THR B 378 " pdb=" C THR B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual -180.00 -133.46 -46.54 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LEU B 661 " pdb=" CA LEU B 661 " ideal model delta harmonic sigma weight residual 180.00 135.77 44.23 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LEU A 661 " pdb=" CA LEU A 661 " ideal model delta harmonic sigma weight residual 180.00 138.04 41.96 0 5.00e+00 4.00e-02 7.04e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1276 0.081 - 0.163: 322 0.163 - 0.244: 46 0.244 - 0.325: 2 0.325 - 0.407: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C2 3PH A 812 " pdb=" C1 3PH A 812 " pdb=" C3 3PH A 812 " pdb=" O21 3PH A 812 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1647 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 587 " -0.035 2.00e-02 2.50e+03 2.34e-02 9.55e+00 pdb=" CG PHE B 587 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 587 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 587 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 587 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 587 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 153 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" CG ASN A 153 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 153 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 153 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 89 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO A 90 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.040 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 174 2.62 - 3.19: 9880 3.19 - 3.76: 16307 3.76 - 4.33: 22979 4.33 - 4.90: 35682 Nonbonded interactions: 85022 Sorted by model distance: nonbonded pdb=" O LEU B 197 " pdb=" NH1 ARG B 203 " model vdw 2.054 3.120 nonbonded pdb=" O LEU A 197 " pdb=" NH1 ARG A 203 " model vdw 2.058 3.120 nonbonded pdb=" OD2 ASP A 606 " pdb=" O HOH A 901 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS B 344 " pdb=" OG SER B 364 " model vdw 2.209 3.120 nonbonded pdb=" OD2 ASP B 606 " pdb=" O HOH B 901 " model vdw 2.236 3.040 ... (remaining 85017 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.410 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.015 0.124 10942 Z= 0.654 Angle : 1.548 12.441 14764 Z= 0.818 Chirality : 0.072 0.407 1650 Planarity : 0.008 0.071 1794 Dihedral : 14.921 87.007 3944 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.25 % Favored : 91.59 % Rotamer: Outliers : 0.37 % Allowed : 2.89 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.17), residues: 1248 helix: -3.82 (0.11), residues: 732 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP A 529 HIS 0.004 0.002 HIS B 27 PHE 0.047 0.005 PHE B 587 TYR 0.034 0.005 TYR B 532 ARG 0.015 0.002 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.31387 ( 503) hydrogen bonds : angle 10.60269 ( 1470) covalent geometry : bond 0.01500 (10924) covalent geometry : angle 1.54759 (14764) Misc. bond : bond 0.00363 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 409 time to evaluate : 1.082 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 43 ASP cc_start: 0.8775 (m-30) cc_final: 0.8317 (m-30) REVERT: A 77 ASN cc_start: 0.8438 (m-40) cc_final: 0.8235 (t0) REVERT: A 95 LYS cc_start: 0.8537 (tttt) cc_final: 0.8118 (tppt) REVERT: A 96 ASN cc_start: 0.8646 (p0) cc_final: 0.8039 (p0) REVERT: A 121 ILE cc_start: 0.9204 (mm) cc_final: 0.8961 (mm) REVERT: A 141 TYR cc_start: 0.8677 (p90) cc_final: 0.8376 (p90) REVERT: A 194 ILE cc_start: 0.8466 (mt) cc_final: 0.8186 (mt) REVERT: A 200 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7792 (ttt90) REVERT: A 210 SER cc_start: 0.8986 (m) cc_final: 0.8595 (p) REVERT: A 220 LEU cc_start: 0.9117 (tp) cc_final: 0.8605 (tt) REVERT: A 238 PHE cc_start: 0.8849 (m-10) cc_final: 0.8628 (m-10) REVERT: A 321 GLN cc_start: 0.8394 (mt0) cc_final: 0.8114 (pp30) REVERT: A 326 MET cc_start: 0.8644 (mmm) cc_final: 0.8439 (tpt) REVERT: A 438 PHE cc_start: 0.7520 (m-80) cc_final: 0.7276 (m-80) REVERT: A 491 TYR cc_start: 0.7373 (t80) cc_final: 0.7067 (t80) REVERT: A 499 PHE cc_start: 0.8788 (m-10) cc_final: 0.8543 (m-80) REVERT: A 602 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7644 (mm-30) REVERT: A 637 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7153 (tm-30) REVERT: A 687 CYS cc_start: 0.5548 (m) cc_final: 0.4490 (t) REVERT: B 95 LYS cc_start: 0.8550 (tttt) cc_final: 0.8111 (tppt) REVERT: B 96 ASN cc_start: 0.8664 (p0) cc_final: 0.8115 (p0) REVERT: B 121 ILE cc_start: 0.9194 (mm) cc_final: 0.8964 (mm) REVERT: B 141 TYR cc_start: 0.8665 (p90) cc_final: 0.8351 (p90) REVERT: B 152 LEU cc_start: 0.8053 (tp) cc_final: 0.7800 (tt) REVERT: B 166 ASP cc_start: 0.8479 (t0) cc_final: 0.7838 (t70) REVERT: B 194 ILE cc_start: 0.8474 (mt) cc_final: 0.8176 (mt) REVERT: B 200 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7786 (ttt90) REVERT: B 210 SER cc_start: 0.8966 (m) cc_final: 0.8617 (p) REVERT: B 220 LEU cc_start: 0.9105 (tp) cc_final: 0.8395 (tt) REVERT: B 497 ASN cc_start: 0.8190 (t0) cc_final: 0.7926 (t0) REVERT: B 499 PHE cc_start: 0.8829 (m-10) cc_final: 0.8553 (m-80) REVERT: B 544 LEU cc_start: 0.7830 (mt) cc_final: 0.7471 (tp) REVERT: B 602 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7626 (mm-30) REVERT: B 606 ASP cc_start: 0.9083 (m-30) cc_final: 0.8403 (m-30) REVERT: B 637 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7156 (tm-30) REVERT: B 683 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7760 (mt-10) outliers start: 4 outliers final: 1 residues processed: 413 average time/residue: 0.2176 time to fit residues: 129.2410 Evaluate side-chains 302 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 613 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 257 GLN A 454 ASN A 618 ASN B 89 GLN B 257 GLN B 454 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.204019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161333 restraints weight = 16245.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165489 restraints weight = 7494.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.168032 restraints weight = 4615.404| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10942 Z= 0.172 Angle : 0.791 10.013 14764 Z= 0.409 Chirality : 0.045 0.212 1650 Planarity : 0.005 0.040 1794 Dihedral : 14.927 77.698 1704 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.42 % Allowed : 11.45 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.20), residues: 1248 helix: -2.37 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -2.05 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 271 HIS 0.001 0.001 HIS A 27 PHE 0.019 0.002 PHE B 624 TYR 0.020 0.002 TYR B 114 ARG 0.006 0.001 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.05614 ( 503) hydrogen bonds : angle 5.77957 ( 1470) covalent geometry : bond 0.00363 (10924) covalent geometry : angle 0.79118 (14764) Misc. bond : bond 0.00145 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 353 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8975 (t0) cc_final: 0.8606 (t0) REVERT: A 95 LYS cc_start: 0.8291 (tttt) cc_final: 0.8004 (tttt) REVERT: A 96 ASN cc_start: 0.8029 (p0) cc_final: 0.7308 (p0) REVERT: A 121 ILE cc_start: 0.8702 (mm) cc_final: 0.8393 (mm) REVERT: A 166 ASP cc_start: 0.7961 (t70) cc_final: 0.6779 (t0) REVERT: A 210 SER cc_start: 0.8788 (m) cc_final: 0.8569 (t) REVERT: A 261 LEU cc_start: 0.8555 (mt) cc_final: 0.8032 (tp) REVERT: A 312 LEU cc_start: 0.9553 (tp) cc_final: 0.9349 (tp) REVERT: A 326 MET cc_start: 0.8469 (mmm) cc_final: 0.8144 (tpt) REVERT: A 372 PHE cc_start: 0.7455 (m-10) cc_final: 0.7036 (t80) REVERT: A 398 ARG cc_start: 0.6674 (mtm-85) cc_final: 0.6437 (mtp180) REVERT: A 542 ILE cc_start: 0.7573 (pt) cc_final: 0.7088 (pt) REVERT: A 637 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7348 (tm-30) REVERT: B 81 LEU cc_start: 0.9142 (tp) cc_final: 0.8917 (tp) REVERT: B 95 LYS cc_start: 0.8307 (tttt) cc_final: 0.8070 (tttt) REVERT: B 96 ASN cc_start: 0.8060 (p0) cc_final: 0.7408 (p0) REVERT: B 121 ILE cc_start: 0.8724 (mm) cc_final: 0.8428 (mm) REVERT: B 141 TYR cc_start: 0.8642 (p90) cc_final: 0.8417 (p90) REVERT: B 152 LEU cc_start: 0.8126 (tp) cc_final: 0.7900 (mt) REVERT: B 210 SER cc_start: 0.8757 (m) cc_final: 0.8550 (t) REVERT: B 261 LEU cc_start: 0.8515 (mt) cc_final: 0.8003 (tp) REVERT: B 354 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8046 (tp) REVERT: B 438 PHE cc_start: 0.7419 (m-80) cc_final: 0.7129 (m-80) REVERT: B 544 LEU cc_start: 0.7645 (mt) cc_final: 0.7262 (tp) REVERT: B 626 LEU cc_start: 0.9282 (mt) cc_final: 0.9000 (mp) REVERT: B 637 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7331 (tm-30) outliers start: 26 outliers final: 12 residues processed: 364 average time/residue: 0.2397 time to fit residues: 125.0449 Evaluate side-chains 304 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 291 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 52 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 134 HIS B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.205933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162988 restraints weight = 16283.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.167230 restraints weight = 7541.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.169811 restraints weight = 4640.036| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10942 Z= 0.143 Angle : 0.693 8.642 14764 Z= 0.354 Chirality : 0.042 0.157 1650 Planarity : 0.004 0.038 1794 Dihedral : 13.809 75.795 1704 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.23 % Allowed : 15.46 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.22), residues: 1248 helix: -1.66 (0.16), residues: 842 sheet: None (None), residues: 0 loop : -1.85 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 271 HIS 0.002 0.001 HIS B 134 PHE 0.031 0.002 PHE A 438 TYR 0.019 0.002 TYR A 173 ARG 0.005 0.001 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 503) hydrogen bonds : angle 5.13534 ( 1470) covalent geometry : bond 0.00303 (10924) covalent geometry : angle 0.69318 (14764) Misc. bond : bond 0.00129 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 1.657 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: A 95 LYS cc_start: 0.8196 (tttt) cc_final: 0.7996 (tttt) REVERT: A 96 ASN cc_start: 0.7915 (p0) cc_final: 0.7279 (p0) REVERT: A 119 GLU cc_start: 0.7275 (tp30) cc_final: 0.7027 (tm-30) REVERT: A 121 ILE cc_start: 0.8745 (mm) cc_final: 0.8437 (mm) REVERT: A 372 PHE cc_start: 0.7388 (m-10) cc_final: 0.7053 (t80) REVERT: A 438 PHE cc_start: 0.7462 (m-80) cc_final: 0.7183 (m-80) REVERT: A 544 LEU cc_start: 0.8534 (mt) cc_final: 0.8161 (tp) REVERT: A 552 ARG cc_start: 0.8021 (tpt170) cc_final: 0.7567 (tpp80) REVERT: A 638 SER cc_start: 0.9141 (p) cc_final: 0.8637 (t) REVERT: A 640 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8042 (ttpt) REVERT: B 76 LEU cc_start: 0.9236 (tp) cc_final: 0.8903 (tt) REVERT: B 96 ASN cc_start: 0.7847 (p0) cc_final: 0.7256 (p0) REVERT: B 121 ILE cc_start: 0.8760 (mm) cc_final: 0.8427 (mm) REVERT: B 141 TYR cc_start: 0.8618 (p90) cc_final: 0.8380 (p90) REVERT: B 152 LEU cc_start: 0.7951 (tp) cc_final: 0.7720 (mt) REVERT: B 354 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7831 (tp) REVERT: B 438 PHE cc_start: 0.7539 (m-80) cc_final: 0.7319 (m-80) REVERT: B 544 LEU cc_start: 0.8110 (mt) cc_final: 0.7761 (tt) outliers start: 24 outliers final: 15 residues processed: 347 average time/residue: 0.2563 time to fit residues: 130.9619 Evaluate side-chains 300 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 242 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.204730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.163257 restraints weight = 16237.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.167393 restraints weight = 7420.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169931 restraints weight = 4516.222| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10942 Z= 0.149 Angle : 0.693 8.764 14764 Z= 0.351 Chirality : 0.043 0.174 1650 Planarity : 0.004 0.033 1794 Dihedral : 13.136 74.612 1704 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.51 % Allowed : 18.81 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.22), residues: 1248 helix: -1.26 (0.16), residues: 852 sheet: None (None), residues: 0 loop : -1.88 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 271 HIS 0.006 0.002 HIS A 134 PHE 0.026 0.002 PHE B 137 TYR 0.020 0.002 TYR A 491 ARG 0.005 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 503) hydrogen bonds : angle 5.00235 ( 1470) covalent geometry : bond 0.00334 (10924) covalent geometry : angle 0.69295 (14764) Misc. bond : bond 0.00118 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 308 time to evaluate : 1.117 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: A 76 LEU cc_start: 0.9154 (tp) cc_final: 0.8830 (tt) REVERT: A 96 ASN cc_start: 0.7839 (p0) cc_final: 0.7203 (p0) REVERT: A 121 ILE cc_start: 0.8784 (mm) cc_final: 0.8458 (mm) REVERT: A 127 THR cc_start: 0.9038 (m) cc_final: 0.8826 (p) REVERT: A 194 ILE cc_start: 0.8472 (mt) cc_final: 0.8186 (mp) REVERT: A 585 GLN cc_start: 0.7905 (mt0) cc_final: 0.7703 (mt0) REVERT: A 590 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7062 (mp) REVERT: A 638 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8790 (t) REVERT: B 76 LEU cc_start: 0.9189 (tp) cc_final: 0.8856 (tt) REVERT: B 96 ASN cc_start: 0.7902 (p0) cc_final: 0.7282 (p0) REVERT: B 121 ILE cc_start: 0.8802 (mm) cc_final: 0.8510 (mm) REVERT: B 127 THR cc_start: 0.9060 (m) cc_final: 0.8801 (p) REVERT: B 141 TYR cc_start: 0.8636 (p90) cc_final: 0.8427 (p90) REVERT: B 152 LEU cc_start: 0.8171 (tp) cc_final: 0.7962 (mt) REVERT: B 194 ILE cc_start: 0.8455 (mt) cc_final: 0.8170 (mp) REVERT: B 212 MET cc_start: 0.8209 (mtp) cc_final: 0.7847 (mtt) REVERT: B 354 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7750 (tp) REVERT: B 372 PHE cc_start: 0.7733 (m-10) cc_final: 0.7382 (m-10) REVERT: B 438 PHE cc_start: 0.7547 (m-80) cc_final: 0.7315 (m-80) REVERT: B 544 LEU cc_start: 0.8463 (mt) cc_final: 0.8229 (tp) outliers start: 27 outliers final: 14 residues processed: 318 average time/residue: 0.2405 time to fit residues: 111.6993 Evaluate side-chains 305 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 288 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 7 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN B 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.206469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.165459 restraints weight = 16160.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.169539 restraints weight = 7489.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.171941 restraints weight = 4550.903| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10942 Z= 0.135 Angle : 0.672 9.015 14764 Z= 0.338 Chirality : 0.041 0.145 1650 Planarity : 0.003 0.032 1794 Dihedral : 12.612 73.965 1704 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.70 % Allowed : 20.11 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.22), residues: 1248 helix: -0.92 (0.16), residues: 850 sheet: None (None), residues: 0 loop : -1.87 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 271 HIS 0.006 0.002 HIS A 134 PHE 0.044 0.002 PHE A 438 TYR 0.020 0.002 TYR A 491 ARG 0.003 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 503) hydrogen bonds : angle 4.88897 ( 1470) covalent geometry : bond 0.00300 (10924) covalent geometry : angle 0.67174 (14764) Misc. bond : bond 0.00127 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9117 (tp) cc_final: 0.8753 (tt) REVERT: A 96 ASN cc_start: 0.7715 (p0) cc_final: 0.7122 (p0) REVERT: A 121 ILE cc_start: 0.8704 (mm) cc_final: 0.8360 (mm) REVERT: A 194 ILE cc_start: 0.8486 (mt) cc_final: 0.8200 (mp) REVERT: A 275 TYR cc_start: 0.8151 (t80) cc_final: 0.7844 (t80) REVERT: A 354 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7389 (tp) REVERT: A 590 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7097 (mp) REVERT: B 76 LEU cc_start: 0.9141 (tp) cc_final: 0.8775 (tt) REVERT: B 96 ASN cc_start: 0.7763 (p0) cc_final: 0.7199 (p0) REVERT: B 121 ILE cc_start: 0.8705 (mm) cc_final: 0.8346 (mm) REVERT: B 152 LEU cc_start: 0.8129 (tp) cc_final: 0.7908 (mt) REVERT: B 194 ILE cc_start: 0.8585 (mt) cc_final: 0.8313 (mp) REVERT: B 543 ARG cc_start: 0.7633 (tmm160) cc_final: 0.7355 (tmm160) REVERT: B 544 LEU cc_start: 0.8364 (mt) cc_final: 0.7485 (mt) outliers start: 29 outliers final: 19 residues processed: 314 average time/residue: 0.2881 time to fit residues: 136.1766 Evaluate side-chains 292 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 499 PHE Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 679 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.0170 chunk 74 optimal weight: 0.5980 chunk 120 optimal weight: 0.0670 chunk 107 optimal weight: 9.9990 chunk 15 optimal weight: 0.0070 chunk 48 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 70 optimal weight: 0.0570 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.0470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS B 89 GLN B 497 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.211197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.168030 restraints weight = 16500.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.172457 restraints weight = 7411.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.175135 restraints weight = 4455.342| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10942 Z= 0.126 Angle : 0.671 9.833 14764 Z= 0.331 Chirality : 0.041 0.162 1650 Planarity : 0.003 0.033 1794 Dihedral : 12.025 73.732 1704 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.68 % Allowed : 22.81 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1248 helix: -0.50 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -1.51 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 271 HIS 0.006 0.001 HIS A 134 PHE 0.052 0.001 PHE A 438 TYR 0.018 0.001 TYR B 141 ARG 0.008 0.001 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 503) hydrogen bonds : angle 4.73451 ( 1470) covalent geometry : bond 0.00265 (10924) covalent geometry : angle 0.67130 (14764) Misc. bond : bond 0.00145 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 2.289 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: A 96 ASN cc_start: 0.7596 (p0) cc_final: 0.6958 (p0) REVERT: A 121 ILE cc_start: 0.8633 (mm) cc_final: 0.8232 (mm) REVERT: A 152 LEU cc_start: 0.8246 (tp) cc_final: 0.8043 (tt) REVERT: A 194 ILE cc_start: 0.8472 (mt) cc_final: 0.8179 (mp) REVERT: A 213 LEU cc_start: 0.9505 (mt) cc_final: 0.9227 (mt) REVERT: A 245 LEU cc_start: 0.8699 (tp) cc_final: 0.8298 (mm) REVERT: A 275 TYR cc_start: 0.8051 (t80) cc_final: 0.7799 (t80) REVERT: A 673 GLU cc_start: 0.7747 (tp30) cc_final: 0.7535 (tp30) REVERT: B 96 ASN cc_start: 0.7652 (p0) cc_final: 0.7003 (p0) REVERT: B 121 ILE cc_start: 0.8649 (mm) cc_final: 0.8268 (mm) REVERT: B 139 ILE cc_start: 0.8621 (mt) cc_final: 0.8363 (pt) REVERT: B 194 ILE cc_start: 0.8573 (mt) cc_final: 0.8333 (mp) REVERT: B 245 LEU cc_start: 0.8693 (tt) cc_final: 0.7742 (mm) REVERT: B 434 TYR cc_start: 0.4401 (OUTLIER) cc_final: 0.3963 (m-80) REVERT: B 438 PHE cc_start: 0.7469 (m-80) cc_final: 0.7255 (m-80) REVERT: B 441 ILE cc_start: 0.5730 (mt) cc_final: 0.5483 (mt) REVERT: B 544 LEU cc_start: 0.8462 (mt) cc_final: 0.8232 (mt) REVERT: B 578 ILE cc_start: 0.8881 (mm) cc_final: 0.8648 (mm) REVERT: B 603 LEU cc_start: 0.7716 (mt) cc_final: 0.7448 (tp) outliers start: 18 outliers final: 12 residues processed: 335 average time/residue: 0.2740 time to fit residues: 134.3133 Evaluate side-chains 305 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 292 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 613 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.209022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.165066 restraints weight = 16878.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.169429 restraints weight = 7712.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.172120 restraints weight = 4647.704| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10942 Z= 0.132 Angle : 0.702 11.723 14764 Z= 0.338 Chirality : 0.041 0.171 1650 Planarity : 0.003 0.030 1794 Dihedral : 11.633 73.419 1704 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.58 % Allowed : 24.49 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1248 helix: -0.33 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -1.44 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.013 0.002 HIS B 134 PHE 0.024 0.001 PHE B 226 TYR 0.027 0.002 TYR B 141 ARG 0.011 0.001 ARG A 543 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 503) hydrogen bonds : angle 4.66442 ( 1470) covalent geometry : bond 0.00297 (10924) covalent geometry : angle 0.70215 (14764) Misc. bond : bond 0.00100 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 298 time to evaluate : 1.053 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: A 96 ASN cc_start: 0.7681 (p0) cc_final: 0.7089 (p0) REVERT: A 111 GLU cc_start: 0.7623 (tp30) cc_final: 0.7189 (tt0) REVERT: A 121 ILE cc_start: 0.8596 (mm) cc_final: 0.8223 (mm) REVERT: A 194 ILE cc_start: 0.8547 (mt) cc_final: 0.8274 (mp) REVERT: A 245 LEU cc_start: 0.8688 (tp) cc_final: 0.8284 (mm) REVERT: B 96 ASN cc_start: 0.7705 (p0) cc_final: 0.7098 (p0) REVERT: B 139 ILE cc_start: 0.8689 (mt) cc_final: 0.8456 (pt) REVERT: B 152 LEU cc_start: 0.8200 (tp) cc_final: 0.7996 (mt) REVERT: B 194 ILE cc_start: 0.8548 (mt) cc_final: 0.8310 (mp) REVERT: B 245 LEU cc_start: 0.8670 (tt) cc_final: 0.7762 (mm) REVERT: B 300 ILE cc_start: 0.9131 (tt) cc_final: 0.8917 (mt) REVERT: B 438 PHE cc_start: 0.7471 (m-80) cc_final: 0.7218 (m-80) REVERT: B 544 LEU cc_start: 0.8482 (mt) cc_final: 0.8219 (mt) outliers start: 17 outliers final: 13 residues processed: 304 average time/residue: 0.2020 time to fit residues: 91.3029 Evaluate side-chains 285 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 542 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS ** B 612 ASN ** 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 = 0.4512 r_free = 0.4512 target = 0.209217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.167995 restraints weight = 16158.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.172215 restraints weight = 7443.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.174709 restraints weight = 4509.558| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10942 Z= 0.136 Angle : 0.714 12.311 14764 Z= 0.343 Chirality : 0.041 0.194 1650 Planarity : 0.003 0.031 1794 Dihedral : 11.493 73.545 1702 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.96 % Allowed : 24.39 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1248 helix: -0.17 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -1.40 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.005 0.001 HIS A 134 PHE 0.025 0.001 PHE B 67 TYR 0.023 0.002 TYR B 141 ARG 0.005 0.000 ARG A 543 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 503) hydrogen bonds : angle 4.67954 ( 1470) covalent geometry : bond 0.00308 (10924) covalent geometry : angle 0.71387 (14764) Misc. bond : bond 0.00096 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 1.192 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: A 96 ASN cc_start: 0.7750 (p0) cc_final: 0.7155 (p0) REVERT: A 111 GLU cc_start: 0.7615 (tp30) cc_final: 0.7178 (tt0) REVERT: A 141 TYR cc_start: 0.8802 (p90) cc_final: 0.8520 (p90) REVERT: A 194 ILE cc_start: 0.8581 (mt) cc_final: 0.8309 (mp) REVERT: A 245 LEU cc_start: 0.8718 (tp) cc_final: 0.8306 (mm) REVERT: B 81 LEU cc_start: 0.8843 (tp) cc_final: 0.8500 (tt) REVERT: B 96 ASN cc_start: 0.7817 (p0) cc_final: 0.7196 (p0) REVERT: B 139 ILE cc_start: 0.8686 (mt) cc_final: 0.8430 (pt) REVERT: B 152 LEU cc_start: 0.8216 (tp) cc_final: 0.8001 (mt) REVERT: B 194 ILE cc_start: 0.8539 (mt) cc_final: 0.8291 (mp) REVERT: B 206 LEU cc_start: 0.9240 (tp) cc_final: 0.8934 (mp) REVERT: B 245 LEU cc_start: 0.8664 (tt) cc_final: 0.7699 (mm) REVERT: B 434 TYR cc_start: 0.4029 (OUTLIER) cc_final: 0.3598 (m-80) REVERT: B 544 LEU cc_start: 0.8459 (mt) cc_final: 0.8193 (mt) REVERT: B 609 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8913 (mt) outliers start: 21 outliers final: 13 residues processed: 295 average time/residue: 0.1963 time to fit residues: 86.3125 Evaluate side-chains 286 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 609 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 61 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** B 612 ASN ** 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 = 0.4524 r_free = 0.4524 target = 0.210078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.166011 restraints weight = 16686.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.170400 restraints weight = 7621.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.173094 restraints weight = 4630.152| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10942 Z= 0.131 Angle : 0.736 18.169 14764 Z= 0.348 Chirality : 0.042 0.437 1650 Planarity : 0.004 0.044 1794 Dihedral : 11.321 78.727 1702 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.40 % Allowed : 24.95 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1248 helix: -0.05 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.36 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 271 HIS 0.009 0.002 HIS B 134 PHE 0.026 0.001 PHE B 226 TYR 0.022 0.002 TYR B 141 ARG 0.008 0.000 ARG A 543 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 503) hydrogen bonds : angle 4.66532 ( 1470) covalent geometry : bond 0.00289 (10924) covalent geometry : angle 0.73605 (14764) Misc. bond : bond 0.00183 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 1.051 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: A 96 ASN cc_start: 0.7681 (p0) cc_final: 0.7094 (p0) REVERT: A 111 GLU cc_start: 0.7492 (tp30) cc_final: 0.7070 (tt0) REVERT: A 139 ILE cc_start: 0.8645 (mt) cc_final: 0.8351 (pt) REVERT: A 141 TYR cc_start: 0.8789 (p90) cc_final: 0.8489 (p90) REVERT: A 194 ILE cc_start: 0.8558 (mt) cc_final: 0.8294 (mp) REVERT: A 206 LEU cc_start: 0.9282 (tp) cc_final: 0.8956 (mp) REVERT: A 275 TYR cc_start: 0.8050 (t80) cc_final: 0.7793 (t80) REVERT: A 312 LEU cc_start: 0.9565 (tp) cc_final: 0.9335 (tp) REVERT: B 96 ASN cc_start: 0.7730 (p0) cc_final: 0.7132 (p0) REVERT: B 139 ILE cc_start: 0.8687 (mt) cc_final: 0.8360 (pt) REVERT: B 152 LEU cc_start: 0.8231 (tp) cc_final: 0.8019 (mt) REVERT: B 194 ILE cc_start: 0.8569 (mt) cc_final: 0.8279 (mp) REVERT: B 206 LEU cc_start: 0.9223 (tp) cc_final: 0.8889 (mp) REVERT: B 245 LEU cc_start: 0.8551 (tt) cc_final: 0.7594 (mm) REVERT: B 434 TYR cc_start: 0.4352 (OUTLIER) cc_final: 0.3917 (m-80) REVERT: B 438 PHE cc_start: 0.7351 (m-80) cc_final: 0.7060 (m-80) REVERT: B 544 LEU cc_start: 0.8453 (mt) cc_final: 0.8195 (mt) REVERT: B 609 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8820 (mt) outliers start: 15 outliers final: 10 residues processed: 280 average time/residue: 0.1896 time to fit residues: 78.1795 Evaluate side-chains 277 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 265 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 609 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 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 = 0.4512 r_free = 0.4512 target = 0.208412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.163922 restraints weight = 16501.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.168231 restraints weight = 7526.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.170851 restraints weight = 4593.459| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10942 Z= 0.145 Angle : 0.740 12.597 14764 Z= 0.352 Chirality : 0.043 0.411 1650 Planarity : 0.004 0.044 1794 Dihedral : 11.288 80.309 1702 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.49 % Allowed : 24.67 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1248 helix: 0.02 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.33 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.009 0.002 HIS B 134 PHE 0.028 0.001 PHE A 226 TYR 0.022 0.002 TYR B 251 ARG 0.008 0.001 ARG A 543 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 503) hydrogen bonds : angle 4.68371 ( 1470) covalent geometry : bond 0.00331 (10924) covalent geometry : angle 0.73995 (14764) Misc. bond : bond 0.00198 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 1.153 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: A 96 ASN cc_start: 0.7815 (p0) cc_final: 0.7220 (p0) REVERT: A 139 ILE cc_start: 0.8639 (mt) cc_final: 0.8269 (pt) REVERT: A 141 TYR cc_start: 0.8775 (p90) cc_final: 0.8530 (p90) REVERT: A 194 ILE cc_start: 0.8620 (mt) cc_final: 0.8326 (mp) REVERT: A 206 LEU cc_start: 0.9280 (tp) cc_final: 0.8955 (mp) REVERT: A 275 TYR cc_start: 0.8113 (t80) cc_final: 0.7848 (t80) REVERT: A 312 LEU cc_start: 0.9572 (tp) cc_final: 0.9344 (tp) REVERT: A 542 ILE cc_start: 0.7143 (pt) cc_final: 0.6675 (pt) REVERT: A 590 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7179 (mp) REVERT: B 96 ASN cc_start: 0.7846 (p0) cc_final: 0.7224 (p0) REVERT: B 139 ILE cc_start: 0.8685 (mt) cc_final: 0.8340 (pt) REVERT: B 194 ILE cc_start: 0.8591 (mt) cc_final: 0.8283 (mp) REVERT: B 206 LEU cc_start: 0.9253 (tp) cc_final: 0.8948 (mp) REVERT: B 245 LEU cc_start: 0.8593 (tt) cc_final: 0.7598 (mm) REVERT: B 300 ILE cc_start: 0.8999 (tt) cc_final: 0.8700 (mt) REVERT: B 434 TYR cc_start: 0.4209 (OUTLIER) cc_final: 0.3710 (m-80) REVERT: B 544 LEU cc_start: 0.8428 (mt) cc_final: 0.8190 (mt) REVERT: B 609 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8895 (mt) outliers start: 16 outliers final: 12 residues processed: 279 average time/residue: 0.1932 time to fit residues: 80.0672 Evaluate side-chains 282 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 267 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 609 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.208519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.167523 restraints weight = 16038.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.171483 restraints weight = 7532.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.173879 restraints weight = 4632.786| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10942 Z= 0.138 Angle : 0.724 11.076 14764 Z= 0.346 Chirality : 0.042 0.353 1650 Planarity : 0.003 0.033 1794 Dihedral : 11.180 79.061 1702 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.12 % Allowed : 25.33 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1248 helix: 0.07 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -1.39 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.009 0.002 HIS B 134 PHE 0.029 0.001 PHE B 226 TYR 0.021 0.002 TYR B 491 ARG 0.004 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 503) hydrogen bonds : angle 4.69115 ( 1470) covalent geometry : bond 0.00311 (10924) covalent geometry : angle 0.72387 (14764) Misc. bond : bond 0.00162 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4142.56 seconds wall clock time: 77 minutes 0.63 seconds (4620.63 seconds total)