Starting phenix.real_space_refine on Sun Aug 24 17:12:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foa_29343/08_2025/8foa_29343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foa_29343/08_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_29343/08_2025/8foa_29343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foa_29343/08_2025/8foa_29343.map" model { file = "/net/cci-nas-00/data/ceres_data/8foa_29343/08_2025/8foa_29343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foa_29343/08_2025/8foa_29343.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.040 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 4} 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-1': 4, 'POV:plan-2': 4, 'POV:plan-3': 5} 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-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 4} 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-1': 4, 'POV:plan-2': 4, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 4.77, per 1000 atoms: 0.22 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: 1.60 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.66 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: 3.25 Time building geometry restraints manager: 2.16 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 21.200 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG D 326 TYR 0.021 0.002 TYR C 467 PHE 0.026 0.003 PHE C 408 TRP 0.027 0.003 TRP D 613 HIS 0.012 0.002 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.02327 (21740) covalent geometry : angle 1.51635 (29290) hydrogen bonds : bond 0.31314 ( 947) hydrogen bonds : angle 8.83579 ( 2730) metal coordination : bond 0.10965 ( 6) *********************** 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 : 0.531 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: 0.6278 time to fit residues: 305.0043 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 : 0.821 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 91 ASN A 118 GLN A 206 GLN A 214 GLN A 261 GLN A 369 GLN A 370 GLN A 418 GLN ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN B 37 ASN B 91 ASN B 122 HIS B 197 ASN B 201 HIS B 206 GLN B 208 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 370 GLN B 418 GLN B 572 ASN B 582 HIS C 122 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 369 GLN C 370 GLN D 40 GLN D 118 GLN D 122 HIS D 197 ASN D 201 HIS D 206 GLN D 208 ASN D 267 GLN D 369 GLN D 370 GLN D 637 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.161728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106319 restraints weight = 28953.185| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.10 r_work: 0.3167 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21746 Z= 0.148 Angle : 0.663 10.424 29290 Z= 0.328 Chirality : 0.041 0.304 3210 Planarity : 0.006 0.064 3544 Dihedral : 19.517 163.396 4497 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.88 % Allowed : 10.83 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.15), residues: 2440 helix: -1.10 (0.12), residues: 1440 sheet: -2.48 (0.50), residues: 96 loop : -2.07 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 140 TYR 0.015 0.001 TYR C 467 PHE 0.016 0.002 PHE C 493 TRP 0.018 0.001 TRP A 321 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00318 (21740) covalent geometry : angle 0.66333 (29290) hydrogen bonds : bond 0.06184 ( 947) hydrogen bonds : angle 4.14761 ( 2730) metal coordination : bond 0.00309 ( 6) *********************** 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 314 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 0.849 Fit side-chains REVERT: A 31 GLN cc_start: 0.7506 (tp-100) cc_final: 0.6993 (pt0) REVERT: A 51 LEU cc_start: 0.8537 (tp) cc_final: 0.8250 (tt) REVERT: A 78 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6820 (mmt) REVERT: A 80 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: A 99 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.7711 (mmt) REVERT: A 189 ILE cc_start: 0.8353 (pt) cc_final: 0.7917 (mt) REVERT: A 222 TYR cc_start: 0.8528 (m-80) cc_final: 0.8261 (m-80) REVERT: A 588 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 62 ASN cc_start: 0.8035 (m110) cc_final: 0.7582 (p0) REVERT: B 214 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: B 491 MET cc_start: 0.8061 (tpp) cc_final: 0.7793 (mmt) REVERT: B 589 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7435 (ptt-90) REVERT: C 99 MET cc_start: 0.8360 (mmt) cc_final: 0.8145 (mmt) REVERT: C 305 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: C 474 MET cc_start: 0.7129 (tpp) cc_final: 0.6733 (OUTLIER) REVERT: D 35 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6503 (tm-30) REVERT: D 41 GLN cc_start: 0.6346 (mm-40) cc_final: 0.5923 (tp40) outliers start: 40 outliers final: 7 residues processed: 299 average time/residue: 0.6231 time to fit residues: 210.1314 Evaluate side-chains 249 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 238 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 99 MET Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain C residue 210 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 33 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 74 GLN A 267 GLN A 426 HIS B 31 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN C 37 ASN C 41 GLN C 74 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 129 ASN D 426 HIS D 546 ASN D 582 HIS D 637 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.158487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102904 restraints weight = 28338.985| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.97 r_work: 0.3106 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21746 Z= 0.165 Angle : 0.623 9.462 29290 Z= 0.308 Chirality : 0.042 0.189 3210 Planarity : 0.005 0.062 3544 Dihedral : 18.220 170.402 4496 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.82 % Allowed : 11.72 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2440 helix: 0.26 (0.13), residues: 1450 sheet: -2.26 (0.56), residues: 80 loop : -1.76 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 140 TYR 0.026 0.002 TYR A 115 PHE 0.015 0.002 PHE C 329 TRP 0.017 0.001 TRP C 593 HIS 0.007 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00396 (21740) covalent geometry : angle 0.62269 (29290) hydrogen bonds : bond 0.05345 ( 947) hydrogen bonds : angle 3.78051 ( 2730) metal coordination : bond 0.00313 ( 6) *********************** 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 313 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.834 Fit side-chains REVERT: A 31 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7163 (pt0) REVERT: A 51 LEU cc_start: 0.8644 (tp) cc_final: 0.8394 (tt) REVERT: A 78 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7052 (mmt) REVERT: A 167 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8736 (tm) REVERT: A 189 ILE cc_start: 0.8424 (pt) cc_final: 0.8131 (mt) REVERT: A 280 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8033 (mt) REVERT: A 300 LYS cc_start: 0.7534 (mttt) cc_final: 0.7266 (mttp) REVERT: A 301 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7685 (ttmt) REVERT: A 331 MET cc_start: 0.8399 (tpt) cc_final: 0.8068 (ttt) REVERT: B 62 ASN cc_start: 0.7991 (m110) cc_final: 0.7576 (p0) REVERT: B 78 MET cc_start: 0.7777 (mpt) cc_final: 0.7475 (mpt) REVERT: B 131 ASN cc_start: 0.8795 (m-40) cc_final: 0.8440 (m-40) REVERT: B 214 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: B 491 MET cc_start: 0.8327 (tpp) cc_final: 0.8097 (mmt) REVERT: C 290 GLN cc_start: 0.8277 (pt0) cc_final: 0.8059 (pt0) REVERT: C 305 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.7712 (mtm-85) REVERT: C 420 ILE cc_start: 0.7608 (tt) cc_final: 0.7061 (mp) REVERT: C 474 MET cc_start: 0.7129 (tpp) cc_final: 0.6587 (tpp) REVERT: D 41 GLN cc_start: 0.6531 (mm-40) cc_final: 0.6120 (tp40) REVERT: D 518 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8075 (tp30) outliers start: 60 outliers final: 16 residues processed: 292 average time/residue: 0.6037 time to fit residues: 200.5539 Evaluate side-chains 251 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 167 LEU 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 B residue 92 LEU Chi-restraints excluded: chain B residue 214 GLN 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 611 CYS Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 404 VAL 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 486 ILE 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 58 optimal weight: 0.5980 chunk 187 optimal weight: 30.0000 chunk 176 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 267 GLN A 637 GLN B 306 GLN B 546 ASN 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 310 GLN D 129 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 = 0.4002 r_free = 0.4002 target = 0.158239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103628 restraints weight = 28181.472| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.26 r_work: 0.3083 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2994 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= 0.143 Angle : 0.588 14.165 29290 Z= 0.288 Chirality : 0.041 0.199 3210 Planarity : 0.004 0.061 3544 Dihedral : 17.389 178.142 4496 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.73 % Allowed : 12.57 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.17), residues: 2440 helix: 0.81 (0.14), residues: 1462 sheet: -1.93 (0.57), residues: 76 loop : -1.65 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 140 TYR 0.017 0.002 TYR D 115 PHE 0.013 0.001 PHE C 329 TRP 0.020 0.001 TRP C 593 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00343 (21740) covalent geometry : angle 0.58797 (29290) hydrogen bonds : bond 0.04718 ( 947) hydrogen bonds : angle 3.61380 ( 2730) metal coordination : bond 0.00158 ( 6) *********************** 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 304 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 0.668 Fit side-chains REVERT: A 31 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7143 (pt0) REVERT: A 51 LEU cc_start: 0.8735 (tp) cc_final: 0.8200 (tm) REVERT: A 78 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6959 (mmt) REVERT: A 80 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 176 GLU cc_start: 0.8280 (mp0) cc_final: 0.8052 (mp0) REVERT: A 189 ILE cc_start: 0.8465 (pt) cc_final: 0.8215 (mt) REVERT: A 280 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 300 LYS cc_start: 0.7473 (mttt) cc_final: 0.7190 (mttp) REVERT: A 331 MET cc_start: 0.8450 (tpt) cc_final: 0.8098 (ttt) REVERT: B 61 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7642 (mp) REVERT: B 62 ASN cc_start: 0.7971 (m110) cc_final: 0.7592 (p0) REVERT: B 131 ASN cc_start: 0.8795 (m-40) cc_final: 0.8454 (m-40) REVERT: B 491 MET cc_start: 0.8288 (tpp) cc_final: 0.8070 (mmt) REVERT: C 290 GLN cc_start: 0.8250 (pt0) cc_final: 0.8038 (pt0) REVERT: C 305 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.7732 (mtm-85) REVERT: C 474 MET cc_start: 0.7194 (tpp) cc_final: 0.6565 (tpp) REVERT: C 596 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.4882 (mm-40) REVERT: C 597 ILE cc_start: 0.8035 (pp) cc_final: 0.7808 (pt) REVERT: D 35 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6542 (tm-30) REVERT: D 41 GLN cc_start: 0.6498 (mm-40) cc_final: 0.6096 (tp40) REVERT: D 518 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8129 (tp30) outliers start: 58 outliers final: 14 residues processed: 287 average time/residue: 0.5170 time to fit residues: 169.9201 Evaluate side-chains 250 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 596 GLN 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 486 ILE Chi-restraints excluded: chain D residue 518 GLU 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 71 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN B 206 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 41 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN D 129 ASN D 418 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.155202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100270 restraints weight = 28472.984| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.97 r_work: 0.3070 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 21746 Z= 0.265 Angle : 0.712 10.141 29290 Z= 0.345 Chirality : 0.047 0.255 3210 Planarity : 0.005 0.057 3544 Dihedral : 17.709 179.049 4496 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.20 % Allowed : 12.90 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2440 helix: 0.76 (0.13), residues: 1470 sheet: -2.09 (0.54), residues: 80 loop : -1.56 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 140 TYR 0.021 0.002 TYR D 115 PHE 0.020 0.002 PHE C 329 TRP 0.023 0.002 TRP C 593 HIS 0.007 0.002 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00654 (21740) covalent geometry : angle 0.71151 (29290) hydrogen bonds : bond 0.05925 ( 947) hydrogen bonds : angle 3.92994 ( 2730) metal coordination : bond 0.00443 ( 6) *********************** 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 302 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 0.816 Fit side-chains REVERT: A 31 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7145 (pt0) REVERT: A 51 LEU cc_start: 0.8615 (tp) cc_final: 0.8294 (tm) REVERT: A 78 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: A 80 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 114 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8748 (tt) REVERT: A 176 GLU cc_start: 0.8347 (mp0) cc_final: 0.8106 (mp0) REVERT: A 189 ILE cc_start: 0.8484 (pt) cc_final: 0.8211 (mt) REVERT: A 280 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 61 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7661 (mp) REVERT: B 62 ASN cc_start: 0.8006 (m110) cc_final: 0.7597 (p0) REVERT: B 131 ASN cc_start: 0.8819 (m-40) cc_final: 0.8481 (m-40) REVERT: B 280 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 491 MET cc_start: 0.8366 (tpp) cc_final: 0.8079 (mmt) REVERT: B 621 ARG cc_start: 0.8328 (tpt-90) cc_final: 0.7966 (tpm170) REVERT: C 65 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7861 (pp) REVERT: C 99 MET cc_start: 0.8454 (mmt) cc_final: 0.8213 (mmt) REVERT: C 222 TYR cc_start: 0.8415 (m-80) cc_final: 0.7492 (m-80) REVERT: C 305 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.7689 (mtm-85) REVERT: C 428 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8051 (mt) REVERT: C 474 MET cc_start: 0.7119 (tpp) cc_final: 0.6535 (tpp) REVERT: C 597 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7970 (pt) REVERT: D 41 GLN cc_start: 0.6591 (mm-40) cc_final: 0.6200 (tp40) REVERT: D 137 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8039 (mt) REVERT: D 139 ARG cc_start: 0.7928 (mpt90) cc_final: 0.7602 (mpt90) REVERT: D 235 VAL cc_start: 0.8737 (t) cc_final: 0.8518 (m) REVERT: D 518 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8107 (tp30) outliers start: 68 outliers final: 23 residues processed: 282 average time/residue: 0.5122 time to fit residues: 165.6605 Evaluate side-chains 257 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 269 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 549 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 137 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 518 GLU Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 217 optimal weight: 5.9990 chunk 135 optimal weight: 0.0470 chunk 184 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN C 290 GLN D 40 GLN D 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.158651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104345 restraints weight = 28258.658| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.96 r_work: 0.3133 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- 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: 27 | |-----------------------------------------------------------------------------| |-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: 0.8597 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21746 Z= 0.116 Angle : 0.574 10.091 29290 Z= 0.279 Chirality : 0.039 0.220 3210 Planarity : 0.004 0.058 3544 Dihedral : 16.614 171.581 4496 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.31 % Allowed : 14.31 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2440 helix: 1.29 (0.14), residues: 1466 sheet: -1.70 (0.57), residues: 76 loop : -1.51 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 140 TYR 0.014 0.001 TYR D 115 PHE 0.012 0.001 PHE C 493 TRP 0.031 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00269 (21740) covalent geometry : angle 0.57408 (29290) hydrogen bonds : bond 0.04237 ( 947) hydrogen bonds : angle 3.54781 ( 2730) metal coordination : bond 0.00138 ( 6) *********************** 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 287 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.769 Fit side-chains REVERT: A 31 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7188 (pt0) REVERT: A 78 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7025 (mmt) REVERT: A 80 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: A 114 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 176 GLU cc_start: 0.8377 (mp0) cc_final: 0.8165 (mp0) REVERT: A 189 ILE cc_start: 0.8466 (pt) cc_final: 0.8237 (mt) REVERT: A 301 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7643 (ttmt) REVERT: A 331 MET cc_start: 0.8365 (tpt) cc_final: 0.8048 (ttp) REVERT: A 481 MET cc_start: 0.8375 (ppp) cc_final: 0.8043 (tmm) REVERT: B 61 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 62 ASN cc_start: 0.7957 (m110) cc_final: 0.7600 (p0) REVERT: B 131 ASN cc_start: 0.8763 (m-40) cc_final: 0.8409 (m-40) REVERT: B 491 MET cc_start: 0.8213 (tpp) cc_final: 0.7988 (mmt) REVERT: C 65 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7845 (pp) REVERT: C 99 MET cc_start: 0.8450 (mmt) cc_final: 0.8147 (mmt) REVERT: C 222 TYR cc_start: 0.8391 (m-80) cc_final: 0.7434 (m-80) REVERT: C 305 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: C 474 MET cc_start: 0.7122 (tpp) cc_final: 0.6564 (tpp) REVERT: C 597 ILE cc_start: 0.8025 (pp) cc_final: 0.7813 (pt) REVERT: C 603 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7652 (mpp) REVERT: D 41 GLN cc_start: 0.6535 (mm-40) cc_final: 0.6236 (tp40) REVERT: D 139 ARG cc_start: 0.7888 (mpt90) cc_final: 0.7408 (mpt90) REVERT: D 228 HIS cc_start: 0.5904 (OUTLIER) cc_final: 0.5354 (m90) REVERT: D 235 VAL cc_start: 0.8721 (t) cc_final: 0.8486 (m) outliers start: 49 outliers final: 22 residues processed: 273 average time/residue: 0.5056 time to fit residues: 158.4354 Evaluate side-chains 255 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 311 THR Chi-restraints excluded: chain A residue 379 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 A residue 622 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 210 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 603 MET 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 228 HIS Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR 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 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 78 optimal weight: 0.3980 chunk 190 optimal weight: 30.0000 chunk 76 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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** B 306 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.158783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103707 restraints weight = 28255.046| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.98 r_work: 0.3120 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 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 = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.082 | | 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: 0.8598 moved from start: 0.3392 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= 0.125 Angle : 0.587 13.211 29290 Z= 0.283 Chirality : 0.040 0.205 3210 Planarity : 0.004 0.060 3544 Dihedral : 16.118 169.719 4496 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.64 % Allowed : 14.50 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2440 helix: 1.50 (0.14), residues: 1452 sheet: -1.62 (0.56), residues: 80 loop : -1.50 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 140 TYR 0.013 0.001 TYR D 115 PHE 0.011 0.001 PHE C 329 TRP 0.030 0.001 TRP C 593 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00292 (21740) covalent geometry : angle 0.58696 (29290) hydrogen bonds : bond 0.04288 ( 947) hydrogen bonds : angle 3.51301 ( 2730) metal coordination : bond 0.00124 ( 6) *********************** 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 290 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7188 (pt0) REVERT: A 65 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8554 (mt) REVERT: A 80 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: A 114 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8775 (tt) REVERT: A 189 ILE cc_start: 0.8465 (pt) cc_final: 0.8253 (mt) REVERT: A 301 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7524 (ttmt) REVERT: A 331 MET cc_start: 0.8359 (tpt) cc_final: 0.8036 (ttt) REVERT: A 414 ARG cc_start: 0.6542 (mtm180) cc_final: 0.6095 (mtt180) REVERT: A 481 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8009 (tmm) REVERT: B 44 ILE cc_start: 0.7600 (mt) cc_final: 0.7265 (mp) REVERT: B 61 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 62 ASN cc_start: 0.7991 (m110) cc_final: 0.7578 (p0) REVERT: B 92 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7389 (tt) REVERT: B 131 ASN cc_start: 0.8803 (m-40) cc_final: 0.8449 (m-40) REVERT: B 306 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: B 491 MET cc_start: 0.8209 (tpp) cc_final: 0.7980 (mmt) REVERT: C 99 MET cc_start: 0.8476 (mmt) cc_final: 0.8190 (mmt) REVERT: C 222 TYR cc_start: 0.8404 (m-80) cc_final: 0.7421 (m-80) REVERT: C 305 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.7683 (mtm-85) REVERT: C 474 MET cc_start: 0.7142 (tpp) cc_final: 0.6612 (tpp) REVERT: C 603 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7645 (mpp) REVERT: C 618 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8598 (pp) REVERT: D 41 GLN cc_start: 0.6542 (mm-40) cc_final: 0.6150 (tp40) REVERT: D 80 GLU cc_start: 0.8618 (pm20) cc_final: 0.7769 (pm20) REVERT: D 137 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7962 (mt) REVERT: D 139 ARG cc_start: 0.7868 (mpt90) cc_final: 0.7396 (mpt90) REVERT: D 235 VAL cc_start: 0.8773 (t) cc_final: 0.8552 (m) REVERT: D 491 MET cc_start: 0.8374 (mmp) cc_final: 0.8137 (mmt) outliers start: 56 outliers final: 25 residues processed: 277 average time/residue: 0.5133 time to fit residues: 161.7976 Evaluate side-chains 259 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 311 THR 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 481 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 622 GLU 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 306 GLN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 210 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 603 MET 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 137 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 131 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** B 306 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106422 restraints weight = 28330.139| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.42 r_work: 0.3100 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21746 Z= 0.114 Angle : 0.578 11.021 29290 Z= 0.278 Chirality : 0.039 0.199 3210 Planarity : 0.004 0.060 3544 Dihedral : 15.778 170.082 4496 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.40 % Allowed : 14.60 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2440 helix: 1.62 (0.14), residues: 1454 sheet: -1.62 (0.56), residues: 80 loop : -1.40 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 140 TYR 0.012 0.001 TYR D 115 PHE 0.011 0.001 PHE C 329 TRP 0.034 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00264 (21740) covalent geometry : angle 0.57796 (29290) hydrogen bonds : bond 0.04070 ( 947) hydrogen bonds : angle 3.46764 ( 2730) metal coordination : bond 0.00105 ( 6) *********************** 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 286 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7717 (tp-100) cc_final: 0.7174 (pt0) REVERT: A 65 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8569 (mt) REVERT: A 78 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7165 (mmt) REVERT: A 80 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: A 114 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 189 ILE cc_start: 0.8463 (pt) cc_final: 0.8259 (mt) REVERT: A 280 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 301 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7493 (ttmt) REVERT: A 331 MET cc_start: 0.8406 (tpt) cc_final: 0.8048 (ttt) REVERT: A 481 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8067 (tmm) REVERT: B 61 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 62 ASN cc_start: 0.7992 (m110) cc_final: 0.7579 (p0) REVERT: B 92 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7345 (tt) REVERT: B 131 ASN cc_start: 0.8795 (m-40) cc_final: 0.8438 (m-40) REVERT: B 306 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: B 491 MET cc_start: 0.8225 (tpp) cc_final: 0.8005 (mmt) REVERT: C 99 MET cc_start: 0.8477 (mmt) cc_final: 0.8192 (mmt) REVERT: C 222 TYR cc_start: 0.8392 (m-80) cc_final: 0.7462 (m-80) REVERT: C 305 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.7701 (mtm-85) REVERT: C 474 MET cc_start: 0.7249 (tpp) cc_final: 0.6676 (tpp) REVERT: C 603 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7689 (mpp) REVERT: C 618 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8581 (pp) REVERT: D 41 GLN cc_start: 0.6447 (mm-40) cc_final: 0.6020 (tp40) REVERT: D 80 GLU cc_start: 0.8578 (pm20) cc_final: 0.7757 (pm20) REVERT: D 137 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7965 (mt) REVERT: D 139 ARG cc_start: 0.7848 (mpt90) cc_final: 0.7370 (mpt90) REVERT: D 235 VAL cc_start: 0.8780 (t) cc_final: 0.8567 (m) REVERT: D 491 MET cc_start: 0.8342 (mmp) cc_final: 0.8129 (mmt) outliers start: 51 outliers final: 27 residues processed: 273 average time/residue: 0.4782 time to fit residues: 149.8401 Evaluate side-chains 263 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 311 THR 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 481 MET 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 181 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 379 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 618 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 404 VAL 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 603 MET 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 137 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 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 98 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 chunk 226 optimal weight: 1.9990 chunk 135 optimal weight: 0.0470 chunk 175 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- 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** A 637 GLN B 128 GLN B 306 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.158425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104349 restraints weight = 28244.996| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.30 r_work: 0.3098 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3520 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= 0.129 Angle : 0.590 11.478 29290 Z= 0.285 Chirality : 0.040 0.196 3210 Planarity : 0.004 0.060 3544 Dihedral : 15.598 168.839 4496 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.64 % Allowed : 14.83 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.18), residues: 2440 helix: 1.64 (0.14), residues: 1458 sheet: -1.62 (0.56), residues: 80 loop : -1.35 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 140 TYR 0.013 0.001 TYR D 115 PHE 0.013 0.001 PHE C 493 TRP 0.035 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00308 (21740) covalent geometry : angle 0.58994 (29290) hydrogen bonds : bond 0.04278 ( 947) hydrogen bonds : angle 3.50550 ( 2730) metal coordination : bond 0.00153 ( 6) *********************** 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 286 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7735 (tp-100) cc_final: 0.7173 (pt0) REVERT: A 65 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8553 (mt) REVERT: A 78 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7172 (mmt) REVERT: A 80 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: A 114 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8755 (tt) REVERT: A 280 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8008 (mt) REVERT: A 301 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7468 (ttmt) REVERT: A 331 MET cc_start: 0.8409 (tpt) cc_final: 0.8062 (ttt) REVERT: A 481 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8091 (tmm) REVERT: B 44 ILE cc_start: 0.7533 (mt) cc_final: 0.7209 (mp) REVERT: B 61 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 62 ASN cc_start: 0.7981 (m110) cc_final: 0.7556 (p0) REVERT: B 92 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7413 (tt) REVERT: B 131 ASN cc_start: 0.8799 (m-40) cc_final: 0.8436 (m-40) REVERT: B 491 MET cc_start: 0.8230 (tpp) cc_final: 0.7999 (mmt) REVERT: C 99 MET cc_start: 0.8479 (mmt) cc_final: 0.8170 (mmt) REVERT: C 222 TYR cc_start: 0.8396 (m-80) cc_final: 0.7457 (m-80) REVERT: C 305 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.7687 (mtm-85) REVERT: C 474 MET cc_start: 0.7244 (tpp) cc_final: 0.6714 (tpp) REVERT: C 603 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7697 (mpp) REVERT: C 618 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8611 (pp) REVERT: D 41 GLN cc_start: 0.6493 (mm-40) cc_final: 0.6088 (tp40) REVERT: D 80 GLU cc_start: 0.8576 (pm20) cc_final: 0.7774 (pm20) REVERT: D 137 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7967 (mt) REVERT: D 139 ARG cc_start: 0.7855 (mpt90) cc_final: 0.7457 (mpt90) REVERT: D 235 VAL cc_start: 0.8809 (t) cc_final: 0.8606 (m) REVERT: D 491 MET cc_start: 0.8363 (mmp) cc_final: 0.8146 (mmt) outliers start: 56 outliers final: 29 residues processed: 271 average time/residue: 0.4992 time to fit residues: 155.6943 Evaluate side-chains 264 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 481 MET 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 181 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 379 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 379 THR Chi-restraints excluded: chain C residue 404 VAL 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 603 MET 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 137 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 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 95 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 129 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 = 0.4007 r_free = 0.4007 target = 0.158719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103824 restraints weight = 28320.449| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 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 = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21746 Z= 0.126 Angle : 0.587 10.806 29290 Z= 0.284 Chirality : 0.040 0.209 3210 Planarity : 0.004 0.061 3544 Dihedral : 15.361 168.078 4496 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.02 % Allowed : 15.54 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2440 helix: 1.69 (0.14), residues: 1456 sheet: -1.62 (0.56), residues: 80 loop : -1.33 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 140 TYR 0.013 0.001 TYR D 115 PHE 0.012 0.001 PHE C 493 TRP 0.042 0.001 TRP C 593 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00300 (21740) covalent geometry : angle 0.58679 (29290) hydrogen bonds : bond 0.04254 ( 947) hydrogen bonds : angle 3.51113 ( 2730) metal coordination : bond 0.00133 ( 6) ********************** 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 275 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7213 (pt0) REVERT: A 78 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7174 (mmt) REVERT: A 80 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: A 114 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8748 (tt) REVERT: A 280 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7986 (mt) REVERT: A 301 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7467 (ttmt) REVERT: A 331 MET cc_start: 0.8375 (tpt) cc_final: 0.8044 (ttt) REVERT: A 481 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8087 (tmm) REVERT: B 44 ILE cc_start: 0.7553 (mt) cc_final: 0.7218 (mp) REVERT: B 61 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7655 (mp) REVERT: B 62 ASN cc_start: 0.7971 (m110) cc_final: 0.7551 (p0) REVERT: B 92 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7384 (tt) REVERT: B 131 ASN cc_start: 0.8794 (m-40) cc_final: 0.8430 (m-40) REVERT: B 491 MET cc_start: 0.8214 (tpp) cc_final: 0.7981 (mmt) REVERT: C 99 MET cc_start: 0.8483 (mmt) cc_final: 0.8165 (mmt) REVERT: C 222 TYR cc_start: 0.8390 (m-80) cc_final: 0.7835 (m-80) REVERT: C 305 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7679 (mtm-85) REVERT: C 474 MET cc_start: 0.7236 (tpp) cc_final: 0.6716 (tpp) REVERT: C 603 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7662 (mpp) REVERT: D 41 GLN cc_start: 0.6499 (mm-40) cc_final: 0.6066 (tp40) REVERT: D 80 GLU cc_start: 0.8565 (pm20) cc_final: 0.7829 (pm20) REVERT: D 137 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7922 (mt) REVERT: D 139 ARG cc_start: 0.7852 (mpt90) cc_final: 0.7458 (mpt90) REVERT: D 235 VAL cc_start: 0.8810 (t) cc_final: 0.8608 (m) REVERT: D 407 ILE cc_start: 0.6763 (tt) cc_final: 0.6428 (tt) outliers start: 43 outliers final: 28 residues processed: 264 average time/residue: 0.5139 time to fit residues: 155.8644 Evaluate side-chains 263 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 481 MET 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 181 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 379 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 183 ILE 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 603 MET Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 137 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 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 115 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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** ** B 306 GLN ** 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 40 GLN D 129 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 = 0.3993 r_free = 0.3993 target = 0.157473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102171 restraints weight = 28442.169| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.99 r_work: 0.3097 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21746 Z= 0.166 Angle : 0.623 11.510 29290 Z= 0.302 Chirality : 0.042 0.215 3210 Planarity : 0.004 0.060 3544 Dihedral : 15.524 166.722 4496 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.26 % Allowed : 15.44 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2440 helix: 1.60 (0.14), residues: 1456 sheet: -1.60 (0.56), residues: 80 loop : -1.36 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 140 TYR 0.014 0.002 TYR D 115 PHE 0.012 0.001 PHE C 553 TRP 0.042 0.001 TRP C 593 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00405 (21740) covalent geometry : angle 0.62312 (29290) hydrogen bonds : bond 0.04790 ( 947) hydrogen bonds : angle 3.61421 ( 2730) metal coordination : bond 0.00244 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8964.93 seconds wall clock time: 152 minutes 35.74 seconds (9155.74 seconds total)