Starting phenix.real_space_refine on Wed Jun 18 19:18:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foa_29343/06_2025/8foa_29343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foa_29343/06_2025/8foa_29343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8foa_29343/06_2025/8foa_29343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foa_29343/06_2025/8foa_29343.map" model { file = "/net/cci-nas-00/data/ceres_data/8foa_29343/06_2025/8foa_29343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foa_29343/06_2025/8foa_29343.cif" } resolution = 2.66 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= 0.040 sd= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 2 6.06 5 P 18 5.49 5 S 160 5.16 5 C 14082 2.51 5 N 3342 2.21 5 O 3682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21287 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "C" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "D" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "A" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 474 Unusual residues: {' CA': 1, ' ZN': 1, 'GEN': 1, 'POV': 9, 'Y01': 4} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 430 Unusual residues: {'POV': 10, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 4, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 314 Unusual residues: {' ZN': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 421 Unusual residues: {'GEN': 1, 'POV': 10, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 4, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 13.90, per 1000 atoms: 0.65 Number of scatterers: 21287 At special positions: 0 Unit cell: (124.32, 127.68, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 1 19.99 S 160 16.00 P 18 15.00 O 3682 8.00 N 3342 7.00 C 14082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 814 " pdb="ZN ZN A 814 " - pdb=" NE2 HIS A 587 " pdb="ZN ZN A 814 " - pdb=" NE2 HIS A 582 " pdb="ZN ZN A 814 " - pdb=" NE2 HIS D 587 " pdb=" ZN C 811 " pdb="ZN ZN C 811 " - pdb=" NE2 HIS C 587 " pdb="ZN ZN C 811 " - pdb=" NE2 HIS C 582 " pdb="ZN ZN C 811 " - pdb=" NE2 HIS B 587 " 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 8 sheets defined 64.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.570A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.858A pdb=" N ASN A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.544A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.150A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.669A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.687A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.646A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.018A pdb=" N ARG A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.629A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.967A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.525A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.855A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.870A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.570A pdb=" N SER A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.650A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.117A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 removed outlier: 3.514A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 423 through 445 removed outlier: 4.217A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.500A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.720A pdb=" N PHE A 468 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 512 removed outlier: 3.542A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 587 removed outlier: 3.903A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 608 removed outlier: 3.874A pdb=" N ILE A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.563A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.674A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.782A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.714A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.615A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.526A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.609A pdb=" N PHE B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.644A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.685A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.804A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.549A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.621A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.591A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.541A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.988A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.582A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 407 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.621A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.609A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.601A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.652A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 512 removed outlier: 3.692A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 577 removed outlier: 4.165A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.641A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 624 removed outlier: 4.033A pdb=" N GLY B 624 " --> pdb=" O ARG B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 624' Processing helix chain 'C' and resid 28 through 44 removed outlier: 3.640A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.600A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.699A pdb=" N ASN C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.705A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.920A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.754A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.802A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.822A pdb=" N ARG C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.785A pdb=" N ARG C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.759A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.543A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.703A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 291 through 298 removed outlier: 4.077A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.512A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.629A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.617A pdb=" N MET C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 334 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 401 removed outlier: 3.526A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.995A pdb=" N ILE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 445 removed outlier: 4.492A pdb=" N VAL C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.700A pdb=" N PHE C 468 " --> pdb=" O ASN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 512 removed outlier: 3.549A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 587 removed outlier: 3.857A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.921A pdb=" N THR C 600 " --> pdb=" O GLN C 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.653A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.617A pdb=" N ASN D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.733A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.855A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.573A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.504A pdb=" N ARG D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.626A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.516A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.856A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.686A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.520A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.518A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.563A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.626A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.689A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.627A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 403 removed outlier: 3.563A pdb=" N ASP D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 removed outlier: 4.097A pdb=" N GLY D 422 " --> pdb=" O GLN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 445 removed outlier: 4.236A pdb=" N VAL D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.733A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.542A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.520A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 512 removed outlier: 3.597A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 577 removed outlier: 4.080A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 Processing helix chain 'D' and resid 588 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.849A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.821A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.768A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 266 through 270 removed outlier: 6.949A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 947 hydrogen bonds defined for protein. 2730 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: 6.59 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 3254 1.29 - 1.45: 5678 1.45 - 1.61: 12423 1.61 - 1.77: 89 1.77 - 1.93: 296 Bond restraints: 21740 Sorted by residual: bond pdb=" CAV Y01 D 805 " pdb=" CAZ Y01 D 805 " ideal model delta sigma weight residual 1.507 1.926 -0.419 2.00e-02 2.50e+03 4.38e+02 bond pdb=" CAV Y01 C 803 " pdb=" CAZ Y01 C 803 " ideal model delta sigma weight residual 1.507 1.924 -0.417 2.00e-02 2.50e+03 4.36e+02 bond pdb=" CAV Y01 B 803 " pdb=" CAZ Y01 B 803 " ideal model delta sigma weight residual 1.507 1.924 -0.417 2.00e-02 2.50e+03 4.36e+02 bond pdb=" CAV Y01 B 804 " pdb=" CAZ Y01 B 804 " ideal model delta sigma weight residual 1.507 1.920 -0.413 2.00e-02 2.50e+03 4.27e+02 bond pdb=" CAV Y01 A 802 " pdb=" CAZ Y01 A 802 " ideal model delta sigma weight residual 1.507 1.914 -0.407 2.00e-02 2.50e+03 4.14e+02 ... (remaining 21735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 28253 3.36 - 6.71: 706 6.71 - 10.07: 231 10.07 - 13.42: 85 13.42 - 16.78: 15 Bond angle restraints: 29290 Sorted by residual: angle pdb=" N PHE D 415 " pdb=" CA PHE D 415 " pdb=" C PHE D 415 " ideal model delta sigma weight residual 113.88 105.12 8.76 1.23e+00 6.61e-01 5.07e+01 angle pdb=" N LYS A 322 " pdb=" CA LYS A 322 " pdb=" C LYS A 322 " ideal model delta sigma weight residual 114.75 107.27 7.48 1.26e+00 6.30e-01 3.52e+01 angle pdb=" C HIS B 228 " pdb=" N LEU B 229 " pdb=" CA LEU B 229 " ideal model delta sigma weight residual 120.54 128.31 -7.77 1.35e+00 5.49e-01 3.31e+01 angle pdb=" N GLU C 622 " pdb=" CA GLU C 622 " pdb=" C GLU C 622 " ideal model delta sigma weight residual 113.72 106.33 7.39 1.30e+00 5.92e-01 3.23e+01 angle pdb=" N ASP B 406 " pdb=" CA ASP B 406 " pdb=" C ASP B 406 " ideal model delta sigma weight residual 114.75 107.65 7.10 1.26e+00 6.30e-01 3.17e+01 ... (remaining 29285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 12834 33.14 - 66.28: 768 66.28 - 99.42: 173 99.42 - 132.56: 58 132.56 - 165.70: 11 Dihedral angle restraints: 13844 sinusoidal: 6684 harmonic: 7160 Sorted by residual: dihedral pdb=" CA ARG A 224 " pdb=" C ARG A 224 " pdb=" N HIS A 225 " pdb=" CA HIS A 225 " ideal model delta harmonic sigma weight residual 180.00 145.46 34.54 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA PHE C 408 " pdb=" C PHE C 408 " pdb=" N ARG C 409 " pdb=" CA ARG C 409 " ideal model delta harmonic sigma weight residual -180.00 -148.16 -31.84 0 5.00e+00 4.00e-02 4.06e+01 dihedral pdb=" CA ASP A 69 " pdb=" C ASP A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 -148.28 -31.72 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 13841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.967: 3162 0.967 - 1.934: 0 1.934 - 2.901: 0 2.901 - 3.868: 1 3.868 - 4.835: 47 Chirality restraints: 3210 Sorted by residual: chirality pdb=" CBC Y01 C 802 " pdb=" CAR Y01 C 802 " pdb=" CAV Y01 C 802 " pdb=" OAW Y01 C 802 " both_signs ideal model delta sigma weight residual False -2.54 2.29 -4.83 2.00e-01 2.50e+01 5.84e+02 chirality pdb=" CBC Y01 A 812 " pdb=" CAR Y01 A 812 " pdb=" CAV Y01 A 812 " pdb=" OAW Y01 A 812 " both_signs ideal model delta sigma weight residual False -2.54 2.28 -4.83 2.00e-01 2.50e+01 5.83e+02 chirality pdb=" CBC Y01 B 802 " pdb=" CAR Y01 B 802 " pdb=" CAV Y01 B 802 " pdb=" OAW Y01 B 802 " both_signs ideal model delta sigma weight residual False -2.54 2.26 -4.80 2.00e-01 2.50e+01 5.77e+02 ... (remaining 3207 not shown) Planarity restraints: 3544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 808 " 0.272 2.00e-02 2.50e+03 3.46e-01 1.20e+03 pdb=" C29 POV C 808 " -0.164 2.00e-02 2.50e+03 pdb="C210 POV C 808 " -0.485 2.00e-02 2.50e+03 pdb="C211 POV C 808 " 0.377 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 809 " 0.130 2.00e-02 2.50e+03 3.38e-01 1.15e+03 pdb=" C29 POV B 809 " -0.424 2.00e-02 2.50e+03 pdb="C210 POV B 809 " 0.477 2.00e-02 2.50e+03 pdb="C211 POV B 809 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 808 " -0.159 2.00e-02 2.50e+03 3.36e-01 1.13e+03 pdb=" C29 POV A 808 " 0.447 2.00e-02 2.50e+03 pdb="C210 POV A 808 " -0.448 2.00e-02 2.50e+03 pdb="C211 POV A 808 " 0.160 2.00e-02 2.50e+03 ... (remaining 3541 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6057 2.82 - 3.34: 18142 3.34 - 3.86: 33147 3.86 - 4.38: 41502 4.38 - 4.90: 69394 Nonbonded interactions: 168242 Sorted by model distance: nonbonded pdb=" O MET A 577 " pdb=" OG1 THR A 581 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 377 " pdb=" OE1 GLU A 389 " model vdw 2.306 3.040 nonbonded pdb=" O LEU A 295 " pdb=" OG1 THR A 299 " model vdw 2.310 3.040 nonbonded pdb=" OE2 GLU C 403 " pdb=" ND1 HIS C 426 " model vdw 2.334 3.120 nonbonded pdb=" O ILE C 597 " pdb=" OG1 THR C 601 " model vdw 2.334 3.040 ... (remaining 168237 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 27 through 638 or (resid 806 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211 or name C212 or name C310 or name C311 or name C312 or n \ ame C313 or name C314 or name C315 or name C316)) or resid 807 or (resid 810 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ )) selection = (chain 'B' and (resid 27 through 638 or resid 806 or (resid 807 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C310 or name C311 or name C312 or name C313)) or resid 810 \ )) selection = (chain 'C' and (resid 27 through 638 or (resid 806 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211 or name C212 or name C310 or name C311 or name C312 or n \ ame C313 or name C314 or name C315 or name C316)) or resid 807 or (resid 810 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C310 or name C311 or name C312 or name C313)) \ )) selection = (chain 'D' and (resid 27 through 638 or (resid 806 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211 or name C212 or name C310 or name C311 or name C312 or n \ ame C313 or name C314 or name C315 or name C316)) or resid 807 or resid 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 53.050 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.023 0.419 21746 Z= 1.158 Angle : 1.516 16.779 29290 Z= 0.688 Chirality : 0.529 4.835 3210 Planarity : 0.013 0.346 3544 Dihedral : 22.530 165.703 9220 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.71 % Rotamer: Outliers : 0.42 % Allowed : 3.67 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -5.28 (0.12), residues: 2440 helix: -4.00 (0.06), residues: 1426 sheet: -2.47 (0.57), residues: 76 loop : -2.40 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 613 HIS 0.012 0.002 HIS D 522 PHE 0.026 0.003 PHE C 408 TYR 0.021 0.002 TYR C 467 ARG 0.008 0.001 ARG D 326 Details of bonding type rmsd hydrogen bonds : bond 0.31314 ( 947) hydrogen bonds : angle 8.83579 ( 2730) metal coordination : bond 0.10965 ( 6) covalent geometry : bond 0.02327 (21740) covalent geometry : angle 1.51635 (29290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 428 time to evaluate : 2.210 Fit side-chains REVERT: A 31 GLN cc_start: 0.7751 (tp40) cc_final: 0.7253 (tt0) REVERT: A 51 LEU cc_start: 0.8637 (tp) cc_final: 0.8008 (tm) REVERT: B 31 GLN cc_start: 0.7932 (tp40) cc_final: 0.7111 (tm-30) REVERT: B 51 LEU cc_start: 0.8741 (tt) cc_final: 0.8534 (tm) REVERT: B 62 ASN cc_start: 0.7937 (m110) cc_final: 0.7318 (p0) REVERT: B 317 VAL cc_start: 0.8790 (t) cc_final: 0.8562 (m) REVERT: B 637 GLN cc_start: 0.7289 (mp-120) cc_final: 0.6776 (mm110) REVERT: C 97 VAL cc_start: 0.8577 (t) cc_final: 0.8245 (p) REVERT: C 305 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7951 (mtt90) REVERT: C 554 MET cc_start: 0.8759 (tpt) cc_final: 0.8507 (tpt) REVERT: D 99 MET cc_start: 0.6791 (mtm) cc_final: 0.6431 (mtp) REVERT: D 114 LEU cc_start: 0.7951 (tp) cc_final: 0.7561 (tm) REVERT: D 129 ASN cc_start: 0.8122 (t0) cc_final: 0.7858 (t0) REVERT: D 130 MET cc_start: 0.7699 (pmm) cc_final: 0.7437 (pmm) outliers start: 9 outliers final: 1 residues processed: 435 average time/residue: 1.4360 time to fit residues: 701.5306 Evaluate side-chains 248 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 37 ASN A 91 ASN A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 214 GLN A 261 GLN A 267 GLN A 369 GLN A 370 GLN A 418 GLN A 637 GLN B 37 ASN B 118 GLN B 122 HIS B 197 ASN B 201 HIS B 208 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 370 GLN B 418 GLN B 572 ASN C 37 ASN C 74 GLN C 122 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN D 37 ASN D 40 GLN D 118 GLN D 122 HIS D 197 ASN D 201 HIS D 208 ASN D 267 GLN D 369 GLN D 370 GLN D 418 GLN D 426 HIS D 582 HIS D 637 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.157993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101832 restraints weight = 28776.235| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.30 r_work: 0.3073 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21746 Z= 0.265 Angle : 0.781 14.569 29290 Z= 0.380 Chirality : 0.048 0.390 3210 Planarity : 0.006 0.063 3544 Dihedral : 19.988 176.977 4497 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.68 % Allowed : 9.98 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.38 (0.15), residues: 2440 helix: -1.14 (0.12), residues: 1460 sheet: -2.43 (0.56), residues: 80 loop : -2.05 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 613 HIS 0.010 0.002 HIS D 522 PHE 0.019 0.002 PHE C 329 TYR 0.022 0.002 TYR C 467 ARG 0.010 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.06587 ( 947) hydrogen bonds : angle 4.27070 ( 2730) metal coordination : bond 0.00395 ( 6) covalent geometry : bond 0.00647 (21740) covalent geometry : angle 0.78117 (29290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 2.478 Fit side-chains REVERT: A 31 GLN cc_start: 0.7520 (tp-100) cc_final: 0.6979 (pt0) REVERT: A 51 LEU cc_start: 0.8560 (tp) cc_final: 0.8284 (tt) REVERT: A 78 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6926 (mmt) REVERT: A 189 ILE cc_start: 0.8410 (pt) cc_final: 0.8003 (mt) REVERT: A 280 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7991 (mt) REVERT: A 378 MET cc_start: 0.8716 (mtm) cc_final: 0.8455 (mtm) REVERT: A 588 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7912 (mm-30) REVERT: B 62 ASN cc_start: 0.8024 (m110) cc_final: 0.7579 (p0) REVERT: B 214 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: B 345 MET cc_start: 0.8679 (mtp) cc_final: 0.8475 (mmm) REVERT: B 491 MET cc_start: 0.8150 (tpp) cc_final: 0.7852 (mmt) REVERT: B 589 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7365 (ptt-90) REVERT: C 99 MET cc_start: 0.8398 (mmt) cc_final: 0.8165 (mmt) REVERT: C 305 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7565 (mtm-85) REVERT: C 474 MET cc_start: 0.7234 (tpp) cc_final: 0.6746 (tpp) REVERT: D 41 GLN cc_start: 0.6452 (mm-40) cc_final: 0.6024 (tp40) REVERT: D 130 MET cc_start: 0.7725 (pmm) cc_final: 0.7488 (pmm) REVERT: D 152 PHE cc_start: 0.8779 (m-80) cc_final: 0.8543 (m-80) REVERT: D 518 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7905 (tp30) outliers start: 57 outliers final: 15 residues processed: 292 average time/residue: 1.4038 time to fit residues: 464.3882 Evaluate side-chains 247 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 518 GLU Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 138 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 267 GLN A 426 HIS B 31 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN D 546 ASN D 637 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103988 restraints weight = 28017.664| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.98 r_work: 0.3127 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21746 Z= 0.129 Angle : 0.587 9.959 29290 Z= 0.290 Chirality : 0.040 0.195 3210 Planarity : 0.005 0.061 3544 Dihedral : 18.222 173.835 4497 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.35 % Allowed : 12.10 % Favored : 85.55 % 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: -0.81 (0.17), residues: 2440 helix: 0.37 (0.13), residues: 1448 sheet: -2.15 (0.56), residues: 80 loop : -1.83 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 593 HIS 0.006 0.001 HIS D 426 PHE 0.015 0.001 PHE C 493 TYR 0.025 0.001 TYR A 115 ARG 0.007 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 947) hydrogen bonds : angle 3.67240 ( 2730) metal coordination : bond 0.00169 ( 6) covalent geometry : bond 0.00302 (21740) covalent geometry : angle 0.58742 (29290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 2.906 Fit side-chains REVERT: A 31 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7169 (pt0) REVERT: A 51 LEU cc_start: 0.8639 (tp) cc_final: 0.8395 (tt) REVERT: A 78 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6969 (mmt) REVERT: A 80 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 189 ILE cc_start: 0.8422 (pt) cc_final: 0.8133 (mt) REVERT: A 300 LYS cc_start: 0.7487 (mttt) cc_final: 0.7207 (mttp) REVERT: A 331 MET cc_start: 0.8373 (tpt) cc_final: 0.8068 (ttp) REVERT: B 62 ASN cc_start: 0.7983 (m110) cc_final: 0.7577 (p0) REVERT: B 78 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7272 (mpt) REVERT: B 123 ILE cc_start: 0.8343 (mm) cc_final: 0.8140 (mm) REVERT: B 131 ASN cc_start: 0.8815 (m-40) cc_final: 0.8441 (m-40) REVERT: B 183 ILE cc_start: 0.8714 (mt) cc_final: 0.8508 (pp) REVERT: B 302 ARG cc_start: 0.7552 (ttt-90) cc_final: 0.7272 (ttt-90) REVERT: C 99 MET cc_start: 0.8389 (mmt) cc_final: 0.8189 (mmt) REVERT: C 290 GLN cc_start: 0.8228 (pt0) cc_final: 0.8010 (pt0) REVERT: C 305 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7656 (mtm-85) REVERT: C 474 MET cc_start: 0.7229 (tpp) cc_final: 0.6660 (tpp) REVERT: D 41 GLN cc_start: 0.6551 (mm-40) cc_final: 0.6122 (tp40) REVERT: D 130 MET cc_start: 0.7850 (pmm) cc_final: 0.7642 (pmm) REVERT: D 518 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8132 (tp30) outliers start: 50 outliers final: 12 residues processed: 282 average time/residue: 1.3493 time to fit residues: 440.3140 Evaluate side-chains 249 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 518 GLU Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 187 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 65 optimal weight: 0.0170 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 637 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN D 637 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.157802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104711 restraints weight = 28193.847| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.34 r_work: 0.3076 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21746 Z= 0.142 Angle : 0.594 12.808 29290 Z= 0.289 Chirality : 0.040 0.178 3210 Planarity : 0.004 0.060 3544 Dihedral : 17.387 179.898 4497 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.82 % Allowed : 12.62 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2440 helix: 0.83 (0.14), residues: 1464 sheet: -1.88 (0.56), residues: 76 loop : -1.66 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 593 HIS 0.006 0.001 HIS D 426 PHE 0.014 0.001 PHE C 329 TYR 0.016 0.002 TYR D 115 ARG 0.010 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 947) hydrogen bonds : angle 3.59933 ( 2730) metal coordination : bond 0.00239 ( 6) covalent geometry : bond 0.00338 (21740) covalent geometry : angle 0.59354 (29290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 2.346 Fit side-chains REVERT: A 31 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7166 (pt0) REVERT: A 51 LEU cc_start: 0.8728 (tp) cc_final: 0.8208 (tm) REVERT: A 78 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6943 (mmt) REVERT: A 80 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: A 189 ILE cc_start: 0.8453 (pt) cc_final: 0.8191 (mt) REVERT: A 280 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8070 (mt) REVERT: A 300 LYS cc_start: 0.7466 (mttt) cc_final: 0.7183 (mttp) REVERT: A 301 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7624 (ttmt) REVERT: A 331 MET cc_start: 0.8428 (tpt) cc_final: 0.8082 (ttt) REVERT: B 61 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7665 (mp) REVERT: B 62 ASN cc_start: 0.7947 (m110) cc_final: 0.7567 (p0) REVERT: B 78 MET cc_start: 0.7840 (mpt) cc_final: 0.7454 (mpt) REVERT: B 131 ASN cc_start: 0.8829 (m-40) cc_final: 0.8483 (m-40) REVERT: B 302 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.7284 (ttm170) REVERT: C 99 MET cc_start: 0.8416 (mmt) cc_final: 0.8193 (mmt) REVERT: C 222 TYR cc_start: 0.8257 (m-80) cc_final: 0.7517 (m-80) REVERT: C 290 GLN cc_start: 0.8264 (pt0) cc_final: 0.8046 (pt0) REVERT: C 305 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.7715 (mtm-85) REVERT: C 474 MET cc_start: 0.7298 (tpp) cc_final: 0.6641 (tpp) REVERT: C 597 ILE cc_start: 0.7991 (pp) cc_final: 0.7743 (pt) REVERT: D 41 GLN cc_start: 0.6516 (mm-40) cc_final: 0.6092 (tp40) outliers start: 60 outliers final: 21 residues processed: 285 average time/residue: 1.3169 time to fit residues: 431.9944 Evaluate side-chains 248 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 234 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS B 91 ASN B 306 GLN C 41 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN D 637 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.159588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105503 restraints weight = 28544.942| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.97 r_work: 0.3152 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 21746 Z= 0.107 Angle : 0.555 10.791 29290 Z= 0.269 Chirality : 0.039 0.179 3210 Planarity : 0.004 0.061 3544 Dihedral : 16.484 179.982 4497 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.45 % Allowed : 13.70 % Favored : 83.85 % 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: 0.27 (0.18), residues: 2440 helix: 1.34 (0.14), residues: 1450 sheet: -1.74 (0.56), residues: 80 loop : -1.58 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 PHE 0.012 0.001 PHE C 493 TYR 0.016 0.001 TYR D 115 ARG 0.010 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 947) hydrogen bonds : angle 3.46262 ( 2730) metal coordination : bond 0.00094 ( 6) covalent geometry : bond 0.00243 (21740) covalent geometry : angle 0.55490 (29290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 2.628 Fit side-chains REVERT: A 31 GLN cc_start: 0.7668 (tp-100) cc_final: 0.7186 (pt0) REVERT: A 51 LEU cc_start: 0.8616 (tp) cc_final: 0.8345 (tm) REVERT: A 78 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6959 (mmt) REVERT: A 80 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: A 96 MET cc_start: 0.8915 (mmm) cc_final: 0.8652 (tpp) REVERT: A 114 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (tt) REVERT: A 189 ILE cc_start: 0.8446 (pt) cc_final: 0.8233 (mt) REVERT: A 301 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7638 (ttmt) REVERT: A 331 MET cc_start: 0.8364 (tpt) cc_final: 0.8057 (ttt) REVERT: B 61 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7686 (mp) REVERT: B 62 ASN cc_start: 0.7942 (m110) cc_final: 0.7567 (p0) REVERT: B 131 ASN cc_start: 0.8747 (m-40) cc_final: 0.8402 (m-40) REVERT: B 302 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7238 (ttm170) REVERT: B 323 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8547 (mtp-110) REVERT: B 621 ARG cc_start: 0.8311 (tpt-90) cc_final: 0.7996 (tpm170) REVERT: C 65 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7843 (pp) REVERT: C 99 MET cc_start: 0.8474 (mmt) cc_final: 0.8265 (mmt) REVERT: C 222 TYR cc_start: 0.8265 (m-80) cc_final: 0.7462 (m-80) REVERT: C 290 GLN cc_start: 0.8234 (pt0) cc_final: 0.8011 (pt0) REVERT: C 305 ARG cc_start: 0.8463 (mtm-85) cc_final: 0.7799 (mtm-85) REVERT: C 474 MET cc_start: 0.7211 (tpp) cc_final: 0.6643 (tpp) REVERT: C 592 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5078 (mt) REVERT: C 618 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8530 (pp) REVERT: D 41 GLN cc_start: 0.6548 (mm-40) cc_final: 0.6162 (tp40) outliers start: 52 outliers final: 17 residues processed: 284 average time/residue: 1.2387 time to fit residues: 405.1347 Evaluate side-chains 250 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 280 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 141 optimal weight: 0.0770 chunk 135 optimal weight: 0.0570 chunk 106 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN B 128 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104976 restraints weight = 28423.158| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.97 r_work: 0.3144 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21746 Z= 0.115 Angle : 0.573 12.674 29290 Z= 0.275 Chirality : 0.039 0.177 3210 Planarity : 0.004 0.060 3544 Dihedral : 16.098 178.185 4497 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.50 % Allowed : 14.45 % Favored : 83.05 % 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: 0.49 (0.18), residues: 2440 helix: 1.52 (0.14), residues: 1454 sheet: -1.73 (0.56), residues: 80 loop : -1.50 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 PHE 0.012 0.001 PHE C 329 TYR 0.015 0.001 TYR D 115 ARG 0.010 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 947) hydrogen bonds : angle 3.46215 ( 2730) metal coordination : bond 0.00138 ( 6) covalent geometry : bond 0.00267 (21740) covalent geometry : angle 0.57332 (29290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7686 (tp-100) cc_final: 0.7179 (pt0) REVERT: A 78 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6888 (mmt) REVERT: A 80 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: A 114 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8794 (tt) REVERT: A 189 ILE cc_start: 0.8455 (pt) cc_final: 0.8245 (mt) REVERT: A 280 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 301 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7606 (ttmt) REVERT: A 331 MET cc_start: 0.8399 (tpt) cc_final: 0.8070 (ttt) REVERT: A 481 MET cc_start: 0.8339 (ppp) cc_final: 0.8015 (tmm) REVERT: B 61 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7685 (mp) REVERT: B 62 ASN cc_start: 0.7957 (m110) cc_final: 0.7580 (p0) REVERT: B 92 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7418 (tt) REVERT: B 131 ASN cc_start: 0.8773 (m-40) cc_final: 0.8412 (m-40) REVERT: B 302 ARG cc_start: 0.7721 (ttt-90) cc_final: 0.7381 (ttm170) REVERT: B 323 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8526 (mtp-110) REVERT: C 65 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7861 (pp) REVERT: C 222 TYR cc_start: 0.8321 (m-80) cc_final: 0.7381 (m-80) REVERT: C 290 GLN cc_start: 0.8259 (pt0) cc_final: 0.8039 (pt0) REVERT: C 305 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7703 (mtm-85) REVERT: C 474 MET cc_start: 0.7241 (tpp) cc_final: 0.6700 (tpp) REVERT: C 618 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8527 (pp) REVERT: D 41 GLN cc_start: 0.6529 (mm-40) cc_final: 0.6134 (tp40) REVERT: D 80 GLU cc_start: 0.8622 (pm20) cc_final: 0.7807 (pm20) REVERT: D 491 MET cc_start: 0.8352 (mmp) cc_final: 0.8141 (mmt) outliers start: 53 outliers final: 24 residues processed: 270 average time/residue: 1.3357 time to fit residues: 415.1065 Evaluate side-chains 257 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 486 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 221 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 546 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN D 637 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105695 restraints weight = 28461.405| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.98 r_work: 0.3155 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 21746 Z= 0.107 Angle : 0.555 9.616 29290 Z= 0.267 Chirality : 0.039 0.175 3210 Planarity : 0.004 0.061 3544 Dihedral : 15.631 178.538 4497 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.64 % Allowed : 14.45 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2440 helix: 1.68 (0.14), residues: 1454 sheet: -1.59 (0.57), residues: 80 loop : -1.41 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 PHE 0.013 0.001 PHE C 493 TYR 0.013 0.001 TYR D 115 ARG 0.011 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 947) hydrogen bonds : angle 3.38322 ( 2730) metal coordination : bond 0.00117 ( 6) covalent geometry : bond 0.00245 (21740) covalent geometry : angle 0.55489 (29290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 2.187 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7168 (pt0) REVERT: A 65 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 78 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6889 (mmt) REVERT: A 80 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: A 114 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8787 (tt) REVERT: A 301 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7453 (ttmt) REVERT: A 331 MET cc_start: 0.8383 (tpt) cc_final: 0.8058 (ttt) REVERT: A 481 MET cc_start: 0.8338 (ppp) cc_final: 0.8056 (tmm) REVERT: B 44 ILE cc_start: 0.7539 (mt) cc_final: 0.7228 (mp) REVERT: B 61 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7683 (mp) REVERT: B 62 ASN cc_start: 0.7957 (m110) cc_final: 0.7595 (p0) REVERT: B 92 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7376 (tt) REVERT: B 131 ASN cc_start: 0.8756 (m-40) cc_final: 0.8450 (m-40) REVERT: B 302 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7467 (ttm170) REVERT: B 323 ARG cc_start: 0.8782 (mtp180) cc_final: 0.8517 (mtp-110) REVERT: C 222 TYR cc_start: 0.8404 (m-80) cc_final: 0.7500 (m-80) REVERT: C 305 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7706 (mtm-85) REVERT: C 474 MET cc_start: 0.7235 (tpp) cc_final: 0.6681 (tpp) REVERT: C 618 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8569 (pp) REVERT: D 41 GLN cc_start: 0.6514 (mm-40) cc_final: 0.6109 (tp40) REVERT: D 80 GLU cc_start: 0.8579 (pm20) cc_final: 0.7789 (pm20) REVERT: D 235 VAL cc_start: 0.8745 (t) cc_final: 0.8528 (m) REVERT: D 491 MET cc_start: 0.8326 (mmp) cc_final: 0.8105 (mmt) outliers start: 56 outliers final: 24 residues processed: 278 average time/residue: 1.2675 time to fit residues: 403.9073 Evaluate side-chains 255 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 486 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 7 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN D 637 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.157676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103027 restraints weight = 28606.511| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.97 r_work: 0.3113 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21746 Z= 0.159 Angle : 0.610 9.871 29290 Z= 0.294 Chirality : 0.041 0.174 3210 Planarity : 0.004 0.059 3544 Dihedral : 15.815 176.280 4497 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.17 % Allowed : 14.92 % Favored : 82.91 % 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: 0.64 (0.18), residues: 2440 helix: 1.57 (0.14), residues: 1464 sheet: -1.64 (0.56), residues: 80 loop : -1.35 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 593 HIS 0.005 0.001 HIS D 426 PHE 0.014 0.001 PHE C 329 TYR 0.014 0.002 TYR D 115 ARG 0.010 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 947) hydrogen bonds : angle 3.56418 ( 2730) metal coordination : bond 0.00243 ( 6) covalent geometry : bond 0.00389 (21740) covalent geometry : angle 0.60976 (29290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 2.506 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7770 (tp-100) cc_final: 0.7200 (pt0) REVERT: A 80 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 114 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8760 (tt) REVERT: A 280 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 301 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7484 (ttmt) REVERT: A 331 MET cc_start: 0.8392 (tpt) cc_final: 0.8084 (ttp) REVERT: A 481 MET cc_start: 0.8392 (ppp) cc_final: 0.8100 (tmm) REVERT: B 61 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7683 (mp) REVERT: B 62 ASN cc_start: 0.7959 (m110) cc_final: 0.7574 (p0) REVERT: B 92 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7390 (tt) REVERT: B 131 ASN cc_start: 0.8765 (m-40) cc_final: 0.8478 (m-40) REVERT: B 302 ARG cc_start: 0.7764 (ttt-90) cc_final: 0.7479 (ttm170) REVERT: C 215 MET cc_start: 0.9193 (tpt) cc_final: 0.8897 (tpt) REVERT: C 222 TYR cc_start: 0.8441 (m-80) cc_final: 0.7510 (m-80) REVERT: C 305 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.7675 (mtm-85) REVERT: C 474 MET cc_start: 0.7287 (tpp) cc_final: 0.6735 (tpp) REVERT: C 618 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8567 (pp) REVERT: D 41 GLN cc_start: 0.6560 (mm-40) cc_final: 0.6160 (tp40) REVERT: D 80 GLU cc_start: 0.8577 (pm20) cc_final: 0.7739 (pm20) REVERT: D 235 VAL cc_start: 0.8755 (t) cc_final: 0.8547 (m) outliers start: 46 outliers final: 25 residues processed: 262 average time/residue: 1.2370 time to fit residues: 372.0423 Evaluate side-chains 252 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 486 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 208 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN D 197 ASN D 637 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.158797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104422 restraints weight = 28486.773| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.97 r_work: 0.3134 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21746 Z= 0.121 Angle : 0.588 16.054 29290 Z= 0.281 Chirality : 0.039 0.190 3210 Planarity : 0.004 0.060 3544 Dihedral : 15.464 173.468 4497 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.02 % Allowed : 15.35 % Favored : 82.63 % 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: 0.79 (0.18), residues: 2440 helix: 1.70 (0.14), residues: 1464 sheet: -1.55 (0.56), residues: 80 loop : -1.29 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 PHE 0.012 0.001 PHE C 329 TYR 0.013 0.001 TYR D 115 ARG 0.012 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 947) hydrogen bonds : angle 3.46964 ( 2730) metal coordination : bond 0.00159 ( 6) covalent geometry : bond 0.00284 (21740) covalent geometry : angle 0.58756 (29290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7206 (pt0) REVERT: A 65 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8528 (mt) REVERT: A 78 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7082 (mmt) REVERT: A 80 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: A 114 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8774 (tt) REVERT: A 280 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8015 (mt) REVERT: A 301 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7420 (ttmt) REVERT: A 331 MET cc_start: 0.8372 (tpt) cc_final: 0.8060 (ttp) REVERT: A 481 MET cc_start: 0.8375 (ppp) cc_final: 0.8079 (tmm) REVERT: B 44 ILE cc_start: 0.7490 (mt) cc_final: 0.7171 (mp) REVERT: B 61 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7650 (mp) REVERT: B 62 ASN cc_start: 0.7970 (m110) cc_final: 0.7571 (p0) REVERT: B 92 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7414 (tt) REVERT: B 131 ASN cc_start: 0.8841 (m-40) cc_final: 0.8533 (m-40) REVERT: B 302 ARG cc_start: 0.7781 (ttt-90) cc_final: 0.7513 (ttm170) REVERT: B 323 ARG cc_start: 0.8792 (mtp180) cc_final: 0.8530 (mtp-110) REVERT: C 215 MET cc_start: 0.9137 (tpt) cc_final: 0.8930 (tpt) REVERT: C 222 TYR cc_start: 0.8436 (m-80) cc_final: 0.7753 (m-80) REVERT: C 305 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.7683 (mtm-85) REVERT: C 428 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 474 MET cc_start: 0.7300 (tpp) cc_final: 0.6688 (tpp) REVERT: C 618 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8608 (pp) REVERT: D 41 GLN cc_start: 0.6506 (mm-40) cc_final: 0.6093 (tp40) REVERT: D 80 GLU cc_start: 0.8559 (pm20) cc_final: 0.7783 (pm20) REVERT: D 235 VAL cc_start: 0.8772 (t) cc_final: 0.8565 (m) outliers start: 43 outliers final: 24 residues processed: 257 average time/residue: 1.2787 time to fit residues: 378.5410 Evaluate side-chains 251 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 159 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 181 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN D 637 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102301 restraints weight = 28535.576| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.96 r_work: 0.3101 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21746 Z= 0.185 Angle : 0.647 14.620 29290 Z= 0.309 Chirality : 0.042 0.211 3210 Planarity : 0.004 0.060 3544 Dihedral : 15.716 169.283 4497 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.02 % Allowed : 15.63 % Favored : 82.34 % 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 (0.18), residues: 2440 helix: 1.50 (0.14), residues: 1476 sheet: -1.54 (0.55), residues: 80 loop : -1.28 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 593 HIS 0.005 0.001 HIS D 426 PHE 0.014 0.002 PHE C 329 TYR 0.015 0.002 TYR D 115 ARG 0.012 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 947) hydrogen bonds : angle 3.62782 ( 2730) metal coordination : bond 0.00290 ( 6) covalent geometry : bond 0.00456 (21740) covalent geometry : angle 0.64693 (29290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7243 (pt0) REVERT: A 65 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8534 (mt) REVERT: A 78 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7256 (mmt) REVERT: A 114 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8762 (tt) REVERT: A 280 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 301 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7426 (ttmt) REVERT: A 331 MET cc_start: 0.8384 (tpt) cc_final: 0.8073 (ttt) REVERT: B 61 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 62 ASN cc_start: 0.7978 (m110) cc_final: 0.7577 (p0) REVERT: B 92 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7384 (tt) REVERT: B 131 ASN cc_start: 0.8883 (m-40) cc_final: 0.8510 (m-40) REVERT: B 302 ARG cc_start: 0.7789 (ttt-90) cc_final: 0.7482 (ttm170) REVERT: C 215 MET cc_start: 0.9130 (tpt) cc_final: 0.8903 (tpt) REVERT: C 222 TYR cc_start: 0.8449 (m-80) cc_final: 0.7454 (m-80) REVERT: C 305 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7691 (mtm-85) REVERT: C 428 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8115 (mt) REVERT: C 474 MET cc_start: 0.7255 (tpp) cc_final: 0.6773 (tpp) REVERT: C 618 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8633 (pp) REVERT: D 41 GLN cc_start: 0.6575 (mm-40) cc_final: 0.6148 (tp40) REVERT: D 80 GLU cc_start: 0.8533 (pm20) cc_final: 0.7756 (pm20) REVERT: D 152 PHE cc_start: 0.8852 (m-80) cc_final: 0.8635 (m-80) REVERT: D 491 MET cc_start: 0.8422 (mmp) cc_final: 0.8214 (mmt) outliers start: 43 outliers final: 25 residues processed: 257 average time/residue: 1.2533 time to fit residues: 369.6014 Evaluate side-chains 252 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 409 ARG Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 486 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 199 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 196 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 93 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN D 637 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108835 restraints weight = 28660.602| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.29 r_work: 0.3123 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 21746 Z= 0.107 Angle : 0.581 15.641 29290 Z= 0.276 Chirality : 0.039 0.201 3210 Planarity : 0.004 0.061 3544 Dihedral : 15.084 172.069 4497 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.84 % Allowed : 16.01 % Favored : 82.16 % 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: 0.93 (0.18), residues: 2440 helix: 1.79 (0.14), residues: 1470 sheet: -1.43 (0.57), residues: 80 loop : -1.24 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 PHE 0.013 0.001 PHE C 493 TYR 0.013 0.001 TYR C 216 ARG 0.013 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 947) hydrogen bonds : angle 3.40348 ( 2730) metal coordination : bond 0.00092 ( 6) covalent geometry : bond 0.00244 (21740) covalent geometry : angle 0.58087 (29290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20863.28 seconds wall clock time: 360 minutes 44.09 seconds (21644.09 seconds total)