Starting phenix.real_space_refine on Wed Jul 30 11:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1p_8960/07_2025/6e1p_8960_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1p_8960/07_2025/6e1p_8960.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/6e1p_8960/07_2025/6e1p_8960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1p_8960/07_2025/6e1p_8960.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1p_8960/07_2025/6e1p_8960_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1p_8960/07_2025/6e1p_8960_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 1632 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 5 9.91 5 P 6 5.49 5 S 46 5.16 5 C 7154 2.51 5 N 1588 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 10697 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5201 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5201 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {' CA': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 147 Unusual residues: {' CA': 3, 'PLM': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 7.29, per 1000 atoms: 0.68 Number of scatterers: 10697 At special positions: 0 Unit cell: (127.638, 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 5 19.99 S 46 16.00 P 6 15.00 O 1898 8.00 N 1588 7.00 C 7154 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 35 through 46 removed outlier: 4.336A pdb=" N ASP A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.599A pdb=" N PHE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.726A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 137 removed outlier: 3.730A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 152 through 173 removed outlier: 3.759A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.624A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.912A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 238 removed outlier: 3.559A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.619A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.523A pdb=" N ILE A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.690A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.624A pdb=" N SER A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.702A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.714A pdb=" N GLU A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 349 through 354 removed outlier: 4.124A pdb=" N GLN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.896A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.572A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 455 removed outlier: 4.120A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 removed outlier: 4.025A pdb=" N ALA A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 486 removed outlier: 4.302A pdb=" N ILE A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.591A pdb=" N TRP A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.675A pdb=" N TRP A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.792A pdb=" N LEU A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 removed outlier: 5.928A pdb=" N ARG A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 551 through 587 removed outlier: 3.750A pdb=" N ILE A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix removed outlier: 4.074A pdb=" N ILE A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.854A pdb=" N PHE A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 601' Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.525A pdb=" N VAL A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.869A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 667 removed outlier: 4.077A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 693 removed outlier: 3.584A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N CYS A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 691 " --> pdb=" O CYS A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 46 removed outlier: 4.324A pdb=" N ASP B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.586A pdb=" N PHE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.506A pdb=" N LEU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.930A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 137 removed outlier: 3.720A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 152 through 173 removed outlier: 3.585A pdb=" N LYS B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.631A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.905A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.701A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.631A pdb=" N LEU B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.523A pdb=" N ILE B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.691A pdb=" N VAL B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Proline residue: B 273 - end of helix removed outlier: 3.581A pdb=" N SER B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.983A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 335 removed outlier: 3.719A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 349 through 355 removed outlier: 4.168A pdb=" N GLN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 removed outlier: 3.568A pdb=" N PHE B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 removed outlier: 3.563A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 455 removed outlier: 3.669A pdb=" N PHE B 438 " --> pdb=" O TYR B 434 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 448 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 475 removed outlier: 4.006A pdb=" N ALA B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.504A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 Processing helix chain 'B' and resid 500 through 513 removed outlier: 3.569A pdb=" N TRP B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 532 removed outlier: 3.800A pdb=" N ILE B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.637A pdb=" N ARG B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 550 removed outlier: 6.088A pdb=" N ARG B 550 " --> pdb=" O ASN B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 551 through 587 removed outlier: 3.514A pdb=" N ALA B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 558 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Proline residue: B 567 - end of helix removed outlier: 4.068A pdb=" N ILE B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 601 removed outlier: 3.904A pdb=" N PHE B 599 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 601' Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 615 through 629 removed outlier: 3.526A pdb=" N VAL B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.866A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.079A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 693 removed outlier: 3.624A pdb=" N LEU B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 680 " --> pdb=" O PHE B 676 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3049 1.34 - 1.46: 2399 1.46 - 1.58: 5400 1.58 - 1.70: 20 1.70 - 1.82: 74 Bond restraints: 10942 Sorted by residual: bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O1P TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 10937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 13970 2.43 - 4.86: 665 4.86 - 7.28: 121 7.28 - 9.71: 43 9.71 - 12.14: 9 Bond angle restraints: 14808 Sorted by residual: angle pdb=" N PHE B 611 " pdb=" CA PHE B 611 " pdb=" CB PHE B 611 " ideal model delta sigma weight residual 110.49 99.93 10.56 1.69e+00 3.50e-01 3.90e+01 angle pdb=" C LEU B 610 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C SER A 150 " pdb=" N ARG A 151 " pdb=" CA ARG A 151 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" N ASN B 612 " pdb=" CA ASN B 612 " pdb=" C ASN B 612 " ideal model delta sigma weight residual 110.80 121.78 -10.98 2.13e+00 2.20e-01 2.66e+01 angle pdb=" C ILE B 371 " pdb=" N PHE B 372 " pdb=" CA PHE B 372 " ideal model delta sigma weight residual 120.79 127.69 -6.90 1.39e+00 5.18e-01 2.46e+01 ... (remaining 14803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 5742 15.01 - 30.02: 425 30.02 - 45.03: 138 45.03 - 60.03: 75 60.03 - 75.04: 2 Dihedral angle restraints: 6382 sinusoidal: 2568 harmonic: 3814 Sorted by residual: dihedral pdb=" CA LEU B 610 " pdb=" C LEU B 610 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " ideal model delta harmonic sigma weight residual -180.00 -130.54 -49.46 0 5.00e+00 4.00e-02 9.79e+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 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE A 611 " pdb=" C PHE A 611 " pdb=" N ASN A 612 " pdb=" CA ASN A 612 " ideal model delta harmonic sigma weight residual -180.00 -137.64 -42.36 0 5.00e+00 4.00e-02 7.18e+01 ... (remaining 6379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1469 0.085 - 0.171: 176 0.171 - 0.256: 19 0.256 - 0.342: 2 0.342 - 0.427: 2 Chirality restraints: 1668 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 2.22 0.43 2.00e-01 2.50e+01 4.57e+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 2.22 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CB TPO A 29 " pdb=" CA TPO A 29 " pdb=" OG1 TPO A 29 " pdb=" CG2 TPO A 29 " both_signs ideal model delta sigma weight residual False 2.48 2.77 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1665 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 613 " 0.027 2.00e-02 2.50e+03 2.10e-02 7.75e+00 pdb=" CG PHE A 613 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 613 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 613 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 613 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 613 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 613 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 89 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO B 90 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 613 " -0.023 2.00e-02 2.50e+03 1.85e-02 5.96e+00 pdb=" CG PHE B 613 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 613 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 613 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 613 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 613 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 613 " -0.005 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 7 2.24 - 2.90: 4238 2.90 - 3.57: 15470 3.57 - 4.23: 24922 4.23 - 4.90: 39996 Nonbonded interactions: 84633 Sorted by model distance: nonbonded pdb=" CC PLM A 809 " pdb=" CA PLM B 804 " model vdw 1.571 3.072 nonbonded pdb=" C3 PLM A 810 " pdb=" C5 PLM B 803 " model vdw 1.742 3.072 nonbonded pdb=" O2P TPO A 26 " pdb=" O1P TPO A 29 " model vdw 2.090 3.040 nonbonded pdb=" OE2 GLU B 450 " pdb=" NH2 ARG B 531 " model vdw 2.179 3.120 nonbonded pdb=" OH TYR B 114 " pdb=" OD2 ASP B 615 " model vdw 2.183 3.040 ... (remaining 84628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 693 or resid 801 or resid 803 through 804 or re \ sid 807 through 810)) selection = (chain 'B' and (resid 22 through 693 or resid 801 or resid 803 through 804 or re \ sid 807 through 810)) } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.060 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.010 0.113 10951 Z= 0.458 Angle : 1.296 12.140 14808 Z= 0.696 Chirality : 0.059 0.427 1668 Planarity : 0.007 0.063 1810 Dihedral : 14.000 75.042 3918 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.95 % Rotamer: Outliers : 0.18 % Allowed : 2.28 % Favored : 97.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -5.32 (0.16), residues: 1262 helix: -3.67 (0.10), residues: 826 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 280 HIS 0.002 0.001 HIS A 416 PHE 0.048 0.004 PHE A 613 TYR 0.029 0.004 TYR A 579 ARG 0.007 0.001 ARG A 540 Details of bonding type rmsd hydrogen bonds : bond 0.30103 ( 503) hydrogen bonds : angle 10.14032 ( 1509) covalent geometry : bond 0.00994 (10942) covalent geometry : angle 1.29634 (14808) Misc. bond : bond 0.03447 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 1.125 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 27 HIS cc_start: 0.8048 (t70) cc_final: 0.7767 (t70) REVERT: A 71 ASP cc_start: 0.9382 (t0) cc_final: 0.8974 (t0) REVERT: A 77 ASN cc_start: 0.9363 (m-40) cc_final: 0.9119 (m110) REVERT: A 89 GLN cc_start: 0.8843 (mt0) cc_final: 0.8426 (mt0) REVERT: A 117 ASN cc_start: 0.9336 (m-40) cc_final: 0.8841 (t0) REVERT: A 137 PHE cc_start: 0.9127 (t80) cc_final: 0.8480 (t80) REVERT: A 195 PHE cc_start: 0.8901 (t80) cc_final: 0.8549 (t80) REVERT: A 204 ASP cc_start: 0.8801 (m-30) cc_final: 0.8529 (m-30) REVERT: A 212 MET cc_start: 0.9066 (ttp) cc_final: 0.8229 (ttp) REVERT: A 307 SER cc_start: 0.9323 (m) cc_final: 0.9099 (t) REVERT: A 320 ASP cc_start: 0.9270 (m-30) cc_final: 0.9037 (m-30) REVERT: A 322 MET cc_start: 0.8509 (tmm) cc_final: 0.8038 (tmm) REVERT: A 326 MET cc_start: 0.9053 (mmm) cc_final: 0.8456 (mmp) REVERT: A 333 LEU cc_start: 0.8218 (tp) cc_final: 0.7952 (tt) REVERT: A 450 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 497 ASN cc_start: 0.8911 (m110) cc_final: 0.8564 (m110) REVERT: A 562 ILE cc_start: 0.8974 (mt) cc_final: 0.8561 (mt) REVERT: A 602 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7937 (mp0) REVERT: A 603 LEU cc_start: 0.8028 (mt) cc_final: 0.7788 (mt) REVERT: A 617 PRO cc_start: 0.8316 (Cg_endo) cc_final: 0.8113 (Cg_exo) REVERT: A 620 MET cc_start: 0.8744 (mmm) cc_final: 0.8536 (tpp) REVERT: A 632 TRP cc_start: 0.8810 (p-90) cc_final: 0.8400 (p-90) REVERT: A 637 GLU cc_start: 0.8132 (tp30) cc_final: 0.7313 (tp30) REVERT: A 641 ASP cc_start: 0.9028 (m-30) cc_final: 0.8591 (t0) REVERT: A 648 SER cc_start: 0.9020 (m) cc_final: 0.8521 (p) REVERT: A 673 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8639 (mm-30) REVERT: A 675 PHE cc_start: 0.8181 (t80) cc_final: 0.7852 (t80) REVERT: A 678 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 27 HIS cc_start: 0.8270 (t70) cc_final: 0.7957 (t70) REVERT: B 71 ASP cc_start: 0.9372 (t0) cc_final: 0.8969 (t0) REVERT: B 77 ASN cc_start: 0.9384 (m-40) cc_final: 0.9144 (m110) REVERT: B 137 PHE cc_start: 0.9134 (t80) cc_final: 0.8509 (t80) REVERT: B 195 PHE cc_start: 0.8876 (t80) cc_final: 0.8585 (t80) REVERT: B 204 ASP cc_start: 0.8796 (m-30) cc_final: 0.8526 (m-30) REVERT: B 212 MET cc_start: 0.9053 (ttp) cc_final: 0.8246 (ttp) REVERT: B 232 TRP cc_start: 0.9084 (t60) cc_final: 0.8710 (t60) REVERT: B 307 SER cc_start: 0.9336 (m) cc_final: 0.9092 (t) REVERT: B 320 ASP cc_start: 0.9284 (m-30) cc_final: 0.9052 (m-30) REVERT: B 322 MET cc_start: 0.8503 (tmm) cc_final: 0.8028 (tmm) REVERT: B 326 MET cc_start: 0.9070 (mmm) cc_final: 0.8467 (mmp) REVERT: B 333 LEU cc_start: 0.8213 (tp) cc_final: 0.7916 (tt) REVERT: B 450 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 497 ASN cc_start: 0.8847 (m110) cc_final: 0.8268 (m110) REVERT: B 542 ILE cc_start: 0.8829 (mt) cc_final: 0.8605 (mt) REVERT: B 602 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7820 (mp0) REVERT: B 635 TRP cc_start: 0.9050 (m-90) cc_final: 0.8743 (m-90) REVERT: B 637 GLU cc_start: 0.8091 (tp30) cc_final: 0.7509 (tp30) REVERT: B 641 ASP cc_start: 0.9030 (m-30) cc_final: 0.8592 (t0) REVERT: B 648 SER cc_start: 0.9037 (m) cc_final: 0.8538 (p) REVERT: B 673 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8647 (mm-30) REVERT: B 675 PHE cc_start: 0.8187 (t80) cc_final: 0.7946 (t80) REVERT: B 681 LEU cc_start: 0.7767 (mt) cc_final: 0.7415 (mt) outliers start: 2 outliers final: 2 residues processed: 490 average time/residue: 0.2152 time to fit residues: 154.3629 Evaluate side-chains 348 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 346 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 440 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 89 GLN A 549 GLN B 89 GLN B 443 ASN B 454 ASN B 549 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.197921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.149869 restraints weight = 18296.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154602 restraints weight = 8311.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.157555 restraints weight = 5097.314| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10951 Z= 0.171 Angle : 0.748 8.543 14808 Z= 0.383 Chirality : 0.044 0.210 1668 Planarity : 0.005 0.041 1810 Dihedral : 13.429 59.592 1628 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 3.10 % Allowed : 15.60 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.88 (0.21), residues: 1262 helix: -1.75 (0.15), residues: 862 sheet: None (None), residues: 0 loop : -1.88 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 232 HIS 0.002 0.001 HIS B 27 PHE 0.021 0.002 PHE B 554 TYR 0.029 0.002 TYR B 532 ARG 0.007 0.001 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.04953 ( 503) hydrogen bonds : angle 5.45313 ( 1509) covalent geometry : bond 0.00363 (10942) covalent geometry : angle 0.74825 (14808) Misc. bond : bond 0.00104 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 427 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.7975 (t70) cc_final: 0.7763 (t70) REVERT: A 71 ASP cc_start: 0.9338 (t0) cc_final: 0.8431 (t0) REVERT: A 137 PHE cc_start: 0.8956 (t80) cc_final: 0.8348 (t80) REVERT: A 151 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7742 (pmt-80) REVERT: A 156 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8978 (mttp) REVERT: A 203 ARG cc_start: 0.9042 (ttp-110) cc_final: 0.8485 (mtm-85) REVERT: A 232 TRP cc_start: 0.8454 (t60) cc_final: 0.8167 (t60) REVERT: A 306 ASP cc_start: 0.8055 (t70) cc_final: 0.7735 (t0) REVERT: A 322 MET cc_start: 0.8482 (tmm) cc_final: 0.8161 (tmm) REVERT: A 324 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7583 (ttt180) REVERT: A 326 MET cc_start: 0.8774 (mmm) cc_final: 0.8334 (mmp) REVERT: A 387 GLU cc_start: 0.9485 (mp0) cc_final: 0.8926 (mm-30) REVERT: A 388 PHE cc_start: 0.8805 (t80) cc_final: 0.8555 (t80) REVERT: A 598 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8901 (tp) REVERT: A 602 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7912 (mp0) REVERT: A 637 GLU cc_start: 0.7826 (tp30) cc_final: 0.7261 (tp30) REVERT: A 641 ASP cc_start: 0.8649 (m-30) cc_final: 0.8279 (t0) REVERT: A 648 SER cc_start: 0.8335 (m) cc_final: 0.8117 (p) REVERT: A 649 ILE cc_start: 0.9099 (mm) cc_final: 0.8885 (mt) REVERT: A 673 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 678 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 71 ASP cc_start: 0.9472 (t0) cc_final: 0.8834 (t0) REVERT: B 137 PHE cc_start: 0.8984 (t80) cc_final: 0.8451 (t80) REVERT: B 322 MET cc_start: 0.8494 (tmm) cc_final: 0.8160 (tmm) REVERT: B 324 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7625 (ttt180) REVERT: B 326 MET cc_start: 0.8844 (mmm) cc_final: 0.8400 (mmp) REVERT: B 387 GLU cc_start: 0.9461 (mp0) cc_final: 0.8752 (mp0) REVERT: B 388 PHE cc_start: 0.8815 (t80) cc_final: 0.8496 (t80) REVERT: B 579 TYR cc_start: 0.9097 (m-80) cc_final: 0.8829 (m-80) REVERT: B 581 SER cc_start: 0.9241 (m) cc_final: 0.8861 (p) REVERT: B 598 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8965 (tt) REVERT: B 602 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7909 (mp0) REVERT: B 610 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8251 (mm) REVERT: B 620 MET cc_start: 0.8534 (tpp) cc_final: 0.8255 (tpp) REVERT: B 637 GLU cc_start: 0.7835 (tp30) cc_final: 0.7369 (tp30) REVERT: B 641 ASP cc_start: 0.8631 (m-30) cc_final: 0.8242 (t0) REVERT: B 648 SER cc_start: 0.8404 (m) cc_final: 0.8154 (p) REVERT: B 673 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8060 (mm-30) REVERT: B 679 LEU cc_start: 0.7685 (tm) cc_final: 0.7427 (tt) outliers start: 34 outliers final: 18 residues processed: 447 average time/residue: 0.2424 time to fit residues: 157.0360 Evaluate side-chains 390 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 368 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 346 GLN B 77 ASN B 315 GLN B 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.200112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153402 restraints weight = 17793.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.158070 restraints weight = 8281.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.160923 restraints weight = 5097.056| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10951 Z= 0.138 Angle : 0.684 9.419 14808 Z= 0.340 Chirality : 0.042 0.161 1668 Planarity : 0.004 0.038 1810 Dihedral : 11.949 59.856 1626 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 4.29 % Allowed : 20.53 % Favored : 75.18 % 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: -2.06 (0.22), residues: 1262 helix: -1.05 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 271 HIS 0.007 0.001 HIS B 27 PHE 0.024 0.001 PHE B 554 TYR 0.019 0.002 TYR B 532 ARG 0.013 0.001 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 503) hydrogen bonds : angle 5.05284 ( 1509) covalent geometry : bond 0.00304 (10942) covalent geometry : angle 0.68390 (14808) Misc. bond : bond 0.00115 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 416 time to evaluate : 1.090 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 39 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: A 137 PHE cc_start: 0.8914 (t80) cc_final: 0.8520 (t80) REVERT: A 151 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7899 (pmt-80) REVERT: A 195 PHE cc_start: 0.8253 (t80) cc_final: 0.8029 (t80) REVERT: A 219 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8410 (tp) REVERT: A 232 TRP cc_start: 0.8449 (t60) cc_final: 0.8110 (t60) REVERT: A 306 ASP cc_start: 0.8093 (t70) cc_final: 0.7804 (t0) REVERT: A 322 MET cc_start: 0.8484 (tmm) cc_final: 0.8119 (tmm) REVERT: A 324 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7716 (ttt180) REVERT: A 326 MET cc_start: 0.8786 (mmm) cc_final: 0.8313 (mmp) REVERT: A 386 ASP cc_start: 0.8958 (p0) cc_final: 0.8706 (p0) REVERT: A 387 GLU cc_start: 0.9410 (mp0) cc_final: 0.9078 (mp0) REVERT: A 388 PHE cc_start: 0.8922 (t80) cc_final: 0.8595 (t80) REVERT: A 602 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7932 (mp0) REVERT: A 637 GLU cc_start: 0.7752 (tp30) cc_final: 0.7206 (tp30) REVERT: A 641 ASP cc_start: 0.8584 (m-30) cc_final: 0.8211 (t0) REVERT: A 648 SER cc_start: 0.8231 (m) cc_final: 0.8004 (p) REVERT: A 649 ILE cc_start: 0.9109 (mm) cc_final: 0.8895 (mt) REVERT: A 673 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 71 ASP cc_start: 0.9423 (t0) cc_final: 0.8829 (t0) REVERT: B 117 ASN cc_start: 0.8948 (m-40) cc_final: 0.8737 (t0) REVERT: B 137 PHE cc_start: 0.8954 (t80) cc_final: 0.8451 (t80) REVERT: B 232 TRP cc_start: 0.8425 (t60) cc_final: 0.8118 (t60) REVERT: B 322 MET cc_start: 0.8463 (tmm) cc_final: 0.8117 (tmm) REVERT: B 324 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7718 (ttt180) REVERT: B 326 MET cc_start: 0.8771 (mmm) cc_final: 0.8327 (mmp) REVERT: B 386 ASP cc_start: 0.8809 (p0) cc_final: 0.8609 (p0) REVERT: B 387 GLU cc_start: 0.9285 (mp0) cc_final: 0.8931 (mp0) REVERT: B 388 PHE cc_start: 0.8890 (t80) cc_final: 0.8619 (t80) REVERT: B 393 GLN cc_start: 0.9076 (tp40) cc_final: 0.8820 (mt0) REVERT: B 579 TYR cc_start: 0.8882 (m-80) cc_final: 0.8664 (m-80) REVERT: B 602 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8042 (mp0) REVERT: B 637 GLU cc_start: 0.7832 (tp30) cc_final: 0.7249 (tp30) REVERT: B 641 ASP cc_start: 0.8596 (m-30) cc_final: 0.8209 (t0) outliers start: 47 outliers final: 27 residues processed: 430 average time/residue: 0.1982 time to fit residues: 124.3701 Evaluate side-chains 391 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 361 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 645 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 105 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.200099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153416 restraints weight = 17635.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157900 restraints weight = 8320.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.160708 restraints weight = 5171.908| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10951 Z= 0.128 Angle : 0.684 8.879 14808 Z= 0.335 Chirality : 0.042 0.149 1668 Planarity : 0.004 0.038 1810 Dihedral : 11.360 58.466 1626 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.28 % Favored : 95.56 % Rotamer: Outliers : 3.56 % Allowed : 22.90 % Favored : 73.54 % 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: -1.37 (0.23), residues: 1262 helix: -0.55 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 271 HIS 0.009 0.001 HIS A 27 PHE 0.018 0.001 PHE B 554 TYR 0.024 0.002 TYR B 656 ARG 0.004 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 503) hydrogen bonds : angle 4.92535 ( 1509) covalent geometry : bond 0.00283 (10942) covalent geometry : angle 0.68432 (14808) Misc. bond : bond 0.00119 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 401 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.9302 (t0) cc_final: 0.8054 (t0) REVERT: A 137 PHE cc_start: 0.8840 (t80) cc_final: 0.8223 (t80) REVERT: A 151 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7957 (pmt-80) REVERT: A 212 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8082 (mtm) REVERT: A 219 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8631 (tp) REVERT: A 306 ASP cc_start: 0.7990 (t70) cc_final: 0.7778 (t0) REVERT: A 322 MET cc_start: 0.8465 (tmm) cc_final: 0.8121 (tmm) REVERT: A 324 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7648 (ttt180) REVERT: A 326 MET cc_start: 0.8810 (mmm) cc_final: 0.8364 (mmp) REVERT: A 333 LEU cc_start: 0.8160 (tt) cc_final: 0.7556 (tp) REVERT: A 386 ASP cc_start: 0.8973 (p0) cc_final: 0.8610 (p0) REVERT: A 387 GLU cc_start: 0.9423 (mp0) cc_final: 0.8910 (mp0) REVERT: A 579 TYR cc_start: 0.8880 (m-80) cc_final: 0.8628 (m-80) REVERT: A 598 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 602 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8070 (mp0) REVERT: A 603 LEU cc_start: 0.8235 (mt) cc_final: 0.7979 (mp) REVERT: A 620 MET cc_start: 0.8102 (tpp) cc_final: 0.7889 (mmm) REVERT: A 632 TRP cc_start: 0.8607 (p-90) cc_final: 0.8308 (p-90) REVERT: A 637 GLU cc_start: 0.7697 (tp30) cc_final: 0.7209 (tp30) REVERT: A 641 ASP cc_start: 0.8583 (m-30) cc_final: 0.8177 (t0) REVERT: A 648 SER cc_start: 0.8222 (m) cc_final: 0.8002 (p) REVERT: A 679 LEU cc_start: 0.7685 (tt) cc_final: 0.7229 (tt) REVERT: B 71 ASP cc_start: 0.9382 (t0) cc_final: 0.8789 (t0) REVERT: B 137 PHE cc_start: 0.8899 (t80) cc_final: 0.8432 (t80) REVERT: B 212 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: B 232 TRP cc_start: 0.8404 (t60) cc_final: 0.8101 (t60) REVERT: B 322 MET cc_start: 0.8470 (tmm) cc_final: 0.8134 (tmm) REVERT: B 324 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7647 (ttt180) REVERT: B 326 MET cc_start: 0.8819 (mmm) cc_final: 0.8380 (mmp) REVERT: B 387 GLU cc_start: 0.9320 (mp0) cc_final: 0.9000 (mp0) REVERT: B 388 PHE cc_start: 0.8883 (t80) cc_final: 0.8668 (t80) REVERT: B 393 GLN cc_start: 0.8960 (tp40) cc_final: 0.8754 (mt0) REVERT: B 546 MET cc_start: 0.6061 (mtm) cc_final: 0.5745 (mtm) REVERT: B 620 MET cc_start: 0.8586 (tpp) cc_final: 0.8345 (tpp) REVERT: B 641 ASP cc_start: 0.8572 (m-30) cc_final: 0.8318 (t0) outliers start: 39 outliers final: 27 residues processed: 416 average time/residue: 0.2407 time to fit residues: 145.9731 Evaluate side-chains 392 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 360 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 114 optimal weight: 0.0010 chunk 90 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.202179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.155399 restraints weight = 17611.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.159959 restraints weight = 8242.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.162735 restraints weight = 5097.174| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10951 Z= 0.120 Angle : 0.674 9.673 14808 Z= 0.326 Chirality : 0.041 0.166 1668 Planarity : 0.004 0.051 1810 Dihedral : 10.766 59.240 1626 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.28 % Allowed : 23.91 % Favored : 72.81 % 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: -0.95 (0.23), residues: 1262 helix: -0.20 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -1.38 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 271 HIS 0.003 0.001 HIS A 27 PHE 0.020 0.001 PHE B 285 TYR 0.025 0.001 TYR B 656 ARG 0.009 0.001 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 503) hydrogen bonds : angle 4.78610 ( 1509) covalent geometry : bond 0.00261 (10942) covalent geometry : angle 0.67440 (14808) Misc. bond : bond 0.00128 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 406 time to evaluate : 1.223 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 137 PHE cc_start: 0.8829 (t80) cc_final: 0.8550 (t80) REVERT: A 151 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7900 (pmt-80) REVERT: A 191 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8706 (mtp85) REVERT: A 212 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7936 (mtm) REVERT: A 219 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 322 MET cc_start: 0.8471 (tmm) cc_final: 0.8122 (tmm) REVERT: A 326 MET cc_start: 0.8830 (mmm) cc_final: 0.8395 (mmp) REVERT: A 386 ASP cc_start: 0.8909 (p0) cc_final: 0.8497 (p0) REVERT: A 387 GLU cc_start: 0.9439 (mp0) cc_final: 0.8935 (mp0) REVERT: A 393 GLN cc_start: 0.9002 (tp40) cc_final: 0.8756 (mt0) REVERT: A 555 ILE cc_start: 0.9079 (mm) cc_final: 0.8802 (pt) REVERT: A 579 TYR cc_start: 0.8856 (m-80) cc_final: 0.8633 (m-80) REVERT: A 632 TRP cc_start: 0.8604 (p-90) cc_final: 0.8289 (p-90) REVERT: A 637 GLU cc_start: 0.7705 (tp30) cc_final: 0.7331 (tp30) REVERT: A 641 ASP cc_start: 0.8597 (m-30) cc_final: 0.8174 (t0) REVERT: A 648 SER cc_start: 0.8225 (m) cc_final: 0.8011 (p) REVERT: A 675 PHE cc_start: 0.8617 (t80) cc_final: 0.8403 (t80) REVERT: B 71 ASP cc_start: 0.9379 (t0) cc_final: 0.8762 (t0) REVERT: B 137 PHE cc_start: 0.8925 (t80) cc_final: 0.8432 (t80) REVERT: B 212 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7963 (mtm) REVERT: B 219 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8687 (tp) REVERT: B 232 TRP cc_start: 0.8414 (t60) cc_final: 0.8117 (t60) REVERT: B 305 TYR cc_start: 0.8927 (t80) cc_final: 0.8609 (t80) REVERT: B 322 MET cc_start: 0.8484 (tmm) cc_final: 0.8150 (tmm) REVERT: B 326 MET cc_start: 0.8862 (mmm) cc_final: 0.8414 (mmp) REVERT: B 387 GLU cc_start: 0.9427 (mp0) cc_final: 0.9010 (mp0) REVERT: B 388 PHE cc_start: 0.8945 (t80) cc_final: 0.8723 (t80) REVERT: B 620 MET cc_start: 0.8760 (tpp) cc_final: 0.8064 (tpp) REVERT: B 641 ASP cc_start: 0.8534 (m-30) cc_final: 0.8278 (t0) outliers start: 36 outliers final: 28 residues processed: 419 average time/residue: 0.2060 time to fit residues: 125.2501 Evaluate side-chains 404 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 65 optimal weight: 10.0000 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.203253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.157320 restraints weight = 17794.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.161880 restraints weight = 8361.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164659 restraints weight = 5139.020| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10951 Z= 0.120 Angle : 0.689 9.846 14808 Z= 0.331 Chirality : 0.041 0.170 1668 Planarity : 0.004 0.051 1810 Dihedral : 10.469 59.190 1624 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.83 % Allowed : 24.54 % Favored : 71.62 % 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: -0.97 (0.23), residues: 1262 helix: -0.18 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.52 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 271 HIS 0.001 0.000 HIS A 27 PHE 0.027 0.001 PHE B 675 TYR 0.021 0.001 TYR B 656 ARG 0.012 0.001 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 503) hydrogen bonds : angle 4.72360 ( 1509) covalent geometry : bond 0.00263 (10942) covalent geometry : angle 0.68880 (14808) Misc. bond : bond 0.00128 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 397 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.9308 (t0) cc_final: 0.8387 (t0) REVERT: A 137 PHE cc_start: 0.8786 (t80) cc_final: 0.8229 (t80) REVERT: A 149 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8079 (p) REVERT: A 151 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7861 (pmt-80) REVERT: A 191 ARG cc_start: 0.8977 (mtt180) cc_final: 0.8765 (mtp85) REVERT: A 212 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8074 (mtm) REVERT: A 232 TRP cc_start: 0.8380 (t60) cc_final: 0.8153 (t60) REVERT: A 322 MET cc_start: 0.8428 (tmm) cc_final: 0.8179 (tmm) REVERT: A 326 MET cc_start: 0.8784 (mmm) cc_final: 0.8339 (mmp) REVERT: A 386 ASP cc_start: 0.8906 (p0) cc_final: 0.8563 (p0) REVERT: A 387 GLU cc_start: 0.9473 (mp0) cc_final: 0.9207 (mm-30) REVERT: A 450 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 632 TRP cc_start: 0.8556 (p-90) cc_final: 0.8283 (p-90) REVERT: A 637 GLU cc_start: 0.7703 (tp30) cc_final: 0.7286 (tp30) REVERT: A 641 ASP cc_start: 0.8537 (m-30) cc_final: 0.8170 (t0) REVERT: A 673 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 71 ASP cc_start: 0.9342 (t0) cc_final: 0.8773 (t0) REVERT: B 137 PHE cc_start: 0.8922 (t80) cc_final: 0.8423 (t80) REVERT: B 212 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7867 (mtm) REVERT: B 232 TRP cc_start: 0.8417 (t60) cc_final: 0.8127 (t60) REVERT: B 322 MET cc_start: 0.8459 (tmm) cc_final: 0.8170 (tmm) REVERT: B 326 MET cc_start: 0.8835 (mmm) cc_final: 0.8409 (mmp) REVERT: B 387 GLU cc_start: 0.9430 (mp0) cc_final: 0.9055 (mt-10) REVERT: B 557 THR cc_start: 0.9276 (t) cc_final: 0.9059 (p) REVERT: B 602 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7210 (tp30) REVERT: B 605 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7078 (mt-10) REVERT: B 620 MET cc_start: 0.8767 (tpp) cc_final: 0.8134 (tpp) REVERT: B 641 ASP cc_start: 0.8507 (m-30) cc_final: 0.8262 (t0) REVERT: B 684 GLU cc_start: 0.7832 (pp20) cc_final: 0.7197 (mm-30) outliers start: 42 outliers final: 31 residues processed: 414 average time/residue: 0.1942 time to fit residues: 116.3186 Evaluate side-chains 399 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 364 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 82 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 585 GLN B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.202591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.156369 restraints weight = 17834.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.160916 restraints weight = 8294.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.163648 restraints weight = 5091.658| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10951 Z= 0.125 Angle : 0.692 10.170 14808 Z= 0.332 Chirality : 0.041 0.182 1668 Planarity : 0.004 0.050 1810 Dihedral : 10.203 58.294 1624 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.01 % Allowed : 24.73 % Favored : 71.26 % 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: -0.84 (0.24), residues: 1262 helix: -0.11 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.39 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 271 HIS 0.001 0.001 HIS B 27 PHE 0.029 0.001 PHE B 285 TYR 0.023 0.001 TYR A 656 ARG 0.009 0.001 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 503) hydrogen bonds : angle 4.68581 ( 1509) covalent geometry : bond 0.00279 (10942) covalent geometry : angle 0.69235 (14808) Misc. bond : bond 0.00125 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 371 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.8768 (t80) cc_final: 0.8493 (t80) REVERT: A 149 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8110 (p) REVERT: A 151 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7797 (pmt-80) REVERT: A 191 ARG cc_start: 0.9014 (mtt180) cc_final: 0.8793 (mtp85) REVERT: A 212 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8273 (mtm) REVERT: A 232 TRP cc_start: 0.8327 (t60) cc_final: 0.8096 (t60) REVERT: A 322 MET cc_start: 0.8450 (tmm) cc_final: 0.8221 (tmm) REVERT: A 326 MET cc_start: 0.8786 (mmm) cc_final: 0.8332 (mmp) REVERT: A 375 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3489 (pp) REVERT: A 386 ASP cc_start: 0.8847 (p0) cc_final: 0.8459 (p0) REVERT: A 387 GLU cc_start: 0.9462 (mp0) cc_final: 0.9171 (mm-30) REVERT: A 632 TRP cc_start: 0.8638 (p-90) cc_final: 0.8366 (p-90) REVERT: A 637 GLU cc_start: 0.7783 (tp30) cc_final: 0.7366 (tp30) REVERT: B 71 ASP cc_start: 0.9309 (t0) cc_final: 0.8686 (t0) REVERT: B 137 PHE cc_start: 0.8861 (t80) cc_final: 0.8443 (t80) REVERT: B 212 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8099 (mtm) REVERT: B 232 TRP cc_start: 0.8468 (t60) cc_final: 0.8173 (t60) REVERT: B 322 MET cc_start: 0.8470 (tmm) cc_final: 0.8219 (tmm) REVERT: B 326 MET cc_start: 0.8782 (mmm) cc_final: 0.8349 (mmp) REVERT: B 341 GLU cc_start: 0.7803 (tp30) cc_final: 0.7161 (tp30) REVERT: B 387 GLU cc_start: 0.9510 (mp0) cc_final: 0.9116 (mm-30) REVERT: B 546 MET cc_start: 0.3347 (mmm) cc_final: 0.3016 (mmm) REVERT: B 557 THR cc_start: 0.9203 (t) cc_final: 0.9001 (p) REVERT: B 602 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7644 (tp30) REVERT: B 684 GLU cc_start: 0.7675 (pp20) cc_final: 0.7169 (mm-30) outliers start: 44 outliers final: 32 residues processed: 392 average time/residue: 0.1997 time to fit residues: 114.0498 Evaluate side-chains 396 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 359 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 96 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 chunk 112 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 0.0470 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.204537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.157460 restraints weight = 17768.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.162068 restraints weight = 8317.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.164852 restraints weight = 5125.193| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10951 Z= 0.121 Angle : 0.717 12.119 14808 Z= 0.339 Chirality : 0.041 0.212 1668 Planarity : 0.004 0.051 1810 Dihedral : 9.810 59.314 1624 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.65 % Allowed : 25.91 % Favored : 70.44 % 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: -0.73 (0.24), residues: 1262 helix: -0.06 (0.18), residues: 892 sheet: None (None), residues: 0 loop : -1.29 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 271 HIS 0.001 0.000 HIS A 134 PHE 0.028 0.001 PHE B 285 TYR 0.024 0.001 TYR A 656 ARG 0.008 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 503) hydrogen bonds : angle 4.60524 ( 1509) covalent geometry : bond 0.00264 (10942) covalent geometry : angle 0.71731 (14808) Misc. bond : bond 0.00125 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 370 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.8742 (t80) cc_final: 0.8480 (t80) REVERT: A 149 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 151 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7991 (pmt-80) REVERT: A 201 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 212 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7702 (ttp) REVERT: A 232 TRP cc_start: 0.8345 (t60) cc_final: 0.8068 (t60) REVERT: A 322 MET cc_start: 0.8439 (tmm) cc_final: 0.8171 (tmm) REVERT: A 326 MET cc_start: 0.8779 (mmm) cc_final: 0.8295 (mmp) REVERT: A 386 ASP cc_start: 0.8896 (p0) cc_final: 0.8525 (p0) REVERT: A 387 GLU cc_start: 0.9473 (mp0) cc_final: 0.9169 (mm-30) REVERT: A 632 TRP cc_start: 0.8615 (p-90) cc_final: 0.8363 (p-90) REVERT: A 637 GLU cc_start: 0.7791 (tp30) cc_final: 0.7399 (tp30) REVERT: A 641 ASP cc_start: 0.8461 (m-30) cc_final: 0.8118 (t0) REVERT: B 71 ASP cc_start: 0.9340 (t0) cc_final: 0.8655 (t0) REVERT: B 137 PHE cc_start: 0.8881 (t80) cc_final: 0.8410 (t80) REVERT: B 212 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7812 (mtm) REVERT: B 232 TRP cc_start: 0.8410 (t60) cc_final: 0.8124 (t60) REVERT: B 322 MET cc_start: 0.8474 (tmm) cc_final: 0.8185 (tmm) REVERT: B 326 MET cc_start: 0.8788 (mmm) cc_final: 0.8355 (mmp) REVERT: B 341 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: B 387 GLU cc_start: 0.9491 (mp0) cc_final: 0.9087 (mm-30) REVERT: B 546 MET cc_start: 0.3253 (mmm) cc_final: 0.2828 (mmm) REVERT: B 684 GLU cc_start: 0.7666 (pp20) cc_final: 0.7206 (mm-30) outliers start: 40 outliers final: 29 residues processed: 388 average time/residue: 0.1909 time to fit residues: 108.6511 Evaluate side-chains 390 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 356 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.202824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155266 restraints weight = 17916.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.159799 restraints weight = 8378.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.162607 restraints weight = 5160.730| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10951 Z= 0.133 Angle : 0.731 10.639 14808 Z= 0.349 Chirality : 0.042 0.243 1668 Planarity : 0.004 0.048 1810 Dihedral : 9.665 58.702 1624 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.74 % Allowed : 26.19 % Favored : 70.07 % 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: -0.63 (0.24), residues: 1262 helix: -0.00 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.17 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 271 HIS 0.002 0.001 HIS A 27 PHE 0.024 0.001 PHE B 285 TYR 0.023 0.001 TYR A 656 ARG 0.006 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 503) hydrogen bonds : angle 4.69138 ( 1509) covalent geometry : bond 0.00300 (10942) covalent geometry : angle 0.73116 (14808) Misc. bond : bond 0.00122 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 1.097 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 137 PHE cc_start: 0.8796 (t80) cc_final: 0.8573 (t80) REVERT: A 149 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 201 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 212 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7899 (ttp) REVERT: A 225 LEU cc_start: 0.9105 (mp) cc_final: 0.8834 (mp) REVERT: A 232 TRP cc_start: 0.8373 (t60) cc_final: 0.8075 (t60) REVERT: A 322 MET cc_start: 0.8441 (tmm) cc_final: 0.8150 (tmm) REVERT: A 326 MET cc_start: 0.8808 (mmm) cc_final: 0.8303 (mmp) REVERT: A 386 ASP cc_start: 0.8899 (p0) cc_final: 0.8554 (p0) REVERT: A 387 GLU cc_start: 0.9472 (mp0) cc_final: 0.9201 (mm-30) REVERT: A 632 TRP cc_start: 0.8600 (p-90) cc_final: 0.8343 (p-90) REVERT: A 637 GLU cc_start: 0.7934 (tp30) cc_final: 0.7395 (tp30) REVERT: A 679 LEU cc_start: 0.7828 (tt) cc_final: 0.7443 (tt) REVERT: B 71 ASP cc_start: 0.9377 (t0) cc_final: 0.8752 (t0) REVERT: B 137 PHE cc_start: 0.8880 (t80) cc_final: 0.8400 (t80) REVERT: B 212 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7805 (mtm) REVERT: B 232 TRP cc_start: 0.8485 (t60) cc_final: 0.8180 (t60) REVERT: B 245 LEU cc_start: 0.8913 (tt) cc_final: 0.8218 (mp) REVERT: B 322 MET cc_start: 0.8491 (tmm) cc_final: 0.8178 (tmm) REVERT: B 326 MET cc_start: 0.8784 (mmm) cc_final: 0.8314 (mmp) REVERT: B 341 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: B 386 ASP cc_start: 0.8964 (p0) cc_final: 0.8524 (p0) REVERT: B 387 GLU cc_start: 0.9496 (mp0) cc_final: 0.9096 (mm-30) REVERT: B 546 MET cc_start: 0.3279 (mmm) cc_final: 0.2717 (mmm) REVERT: B 632 TRP cc_start: 0.8563 (p-90) cc_final: 0.8329 (p-90) REVERT: B 679 LEU cc_start: 0.7908 (tt) cc_final: 0.7586 (tt) outliers start: 41 outliers final: 33 residues processed: 370 average time/residue: 0.2067 time to fit residues: 113.3248 Evaluate side-chains 390 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 353 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 0.9990 chunk 97 optimal weight: 0.0020 chunk 90 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 88 optimal weight: 0.0570 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.4506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.204640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.157477 restraints weight = 17667.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.162059 restraints weight = 8247.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.164824 restraints weight = 5072.627| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10951 Z= 0.124 Angle : 0.745 11.336 14808 Z= 0.352 Chirality : 0.042 0.271 1668 Planarity : 0.004 0.047 1810 Dihedral : 9.229 58.808 1624 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.65 % Allowed : 27.37 % Favored : 68.98 % 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: -0.60 (0.24), residues: 1262 helix: 0.02 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 271 HIS 0.002 0.001 HIS A 27 PHE 0.038 0.001 PHE B 171 TYR 0.023 0.001 TYR A 656 ARG 0.007 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 503) hydrogen bonds : angle 4.67573 ( 1509) covalent geometry : bond 0.00275 (10942) covalent geometry : angle 0.74543 (14808) Misc. bond : bond 0.00123 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 365 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.8780 (t80) cc_final: 0.8576 (t80) REVERT: A 149 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8160 (p) REVERT: A 151 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8094 (pmt-80) REVERT: A 152 LEU cc_start: 0.8947 (mp) cc_final: 0.8712 (pt) REVERT: A 225 LEU cc_start: 0.9075 (mp) cc_final: 0.8839 (mp) REVERT: A 232 TRP cc_start: 0.8336 (t60) cc_final: 0.8027 (t60) REVERT: A 322 MET cc_start: 0.8535 (tmm) cc_final: 0.8224 (tmm) REVERT: A 326 MET cc_start: 0.8783 (mmm) cc_final: 0.8294 (mmp) REVERT: A 386 ASP cc_start: 0.8875 (p0) cc_final: 0.8423 (p0) REVERT: A 387 GLU cc_start: 0.9468 (mp0) cc_final: 0.8928 (mp0) REVERT: A 598 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8920 (tt) REVERT: A 632 TRP cc_start: 0.8572 (p-90) cc_final: 0.8292 (p-90) REVERT: A 637 GLU cc_start: 0.7911 (tp30) cc_final: 0.7374 (tp30) REVERT: A 684 GLU cc_start: 0.7543 (pp20) cc_final: 0.6627 (tp30) REVERT: B 71 ASP cc_start: 0.9306 (t0) cc_final: 0.8675 (t0) REVERT: B 137 PHE cc_start: 0.8874 (t80) cc_final: 0.8407 (t80) REVERT: B 200 ARG cc_start: 0.8193 (ptt-90) cc_final: 0.7908 (ptp90) REVERT: B 201 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 212 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8091 (ttm) REVERT: B 232 TRP cc_start: 0.8455 (t60) cc_final: 0.8164 (t60) REVERT: B 322 MET cc_start: 0.8484 (tmm) cc_final: 0.8206 (tmm) REVERT: B 326 MET cc_start: 0.8784 (mmm) cc_final: 0.8364 (mmp) REVERT: B 341 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: B 387 GLU cc_start: 0.9461 (mp0) cc_final: 0.9124 (mm-30) REVERT: B 546 MET cc_start: 0.3578 (mmm) cc_final: 0.3099 (mmm) REVERT: B 632 TRP cc_start: 0.8537 (p-90) cc_final: 0.8324 (p-90) REVERT: B 684 GLU cc_start: 0.7383 (pp20) cc_final: 0.6791 (tp30) outliers start: 40 outliers final: 30 residues processed: 382 average time/residue: 0.1874 time to fit residues: 105.0258 Evaluate side-chains 391 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 0.4980 chunk 94 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.204291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156112 restraints weight = 18210.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.160906 restraints weight = 8323.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.163807 restraints weight = 5100.088| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10951 Z= 0.126 Angle : 0.738 10.777 14808 Z= 0.351 Chirality : 0.042 0.269 1668 Planarity : 0.004 0.044 1810 Dihedral : 8.931 56.947 1624 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.28 % Allowed : 27.92 % Favored : 68.80 % 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: -0.54 (0.24), residues: 1262 helix: 0.05 (0.18), residues: 894 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 271 HIS 0.003 0.001 HIS A 27 PHE 0.019 0.001 PHE B 285 TYR 0.022 0.001 TYR A 656 ARG 0.007 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 503) hydrogen bonds : angle 4.67090 ( 1509) covalent geometry : bond 0.00278 (10942) covalent geometry : angle 0.73823 (14808) Misc. bond : bond 0.00121 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.54 seconds wall clock time: 76 minutes 56.44 seconds (4616.44 seconds total)