Starting phenix.real_space_refine on Tue Dec 31 04:32:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ogl_12883/12_2024/7ogl_12883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ogl_12883/12_2024/7ogl_12883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ogl_12883/12_2024/7ogl_12883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ogl_12883/12_2024/7ogl_12883.map" model { file = "/net/cci-nas-00/data/ceres_data/7ogl_12883/12_2024/7ogl_12883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ogl_12883/12_2024/7ogl_12883.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 9269 2.51 5 N 2602 2.21 5 O 2833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14763 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 4899 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 28, 'TRANS': 660} Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 453 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 211 Chain: "B" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 4933 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 270 Chain: "C" Number of atoms: 4928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 4928 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 269 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.99, per 1000 atoms: 0.61 Number of scatterers: 14763 At special positions: 0 Unit cell: (109.695, 110.76, 139.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 2833 8.00 N 2602 7.00 C 9269 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: 3.91 Conformation dependent library (CDL) restraints added in 2.4 seconds 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3786 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 19 sheets defined 37.6% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 85 through 100 removed outlier: 4.330A pdb=" N ILE A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.697A pdb=" N ILE A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.889A pdb=" N GLU A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.677A pdb=" N GLN A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.595A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 258 removed outlier: 5.013A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 3.513A pdb=" N LEU A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 312 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.886A pdb=" N GLU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 515 through 541 removed outlier: 3.577A pdb=" N GLY A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 601 through 618 removed outlier: 3.577A pdb=" N ALA A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 85 through 100 removed outlier: 4.330A pdb=" N ILE B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 126 through 141 removed outlier: 3.743A pdb=" N ILE B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.889A pdb=" N GLU B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.678A pdb=" N GLN B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.595A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 5.013A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 3.513A pdb=" N LEU B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 312 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 397 through 413 removed outlier: 3.777A pdb=" N HIS B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 515 through 541 removed outlier: 3.577A pdb=" N GLY B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 564 Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.587A pdb=" N ALA B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 85 through 100 removed outlier: 4.330A pdb=" N ILE C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 126 through 141 removed outlier: 3.744A pdb=" N ILE C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.889A pdb=" N GLU C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.678A pdb=" N GLN C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.595A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 258 removed outlier: 5.013A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 3.512A pdb=" N LEU C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.570A pdb=" N ALA C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 397 through 413 removed outlier: 3.566A pdb=" N ILE C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.577A pdb=" N GLY C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 564 Processing helix chain 'C' and resid 565 through 570 removed outlier: 4.209A pdb=" N ILE C 569 " --> pdb=" O ILE C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 601 through 616 removed outlier: 3.586A pdb=" N ALA C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 655 removed outlier: 4.600A pdb=" N ALA C 655 " --> pdb=" O ILE C 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 651 through 655' Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.615A pdb=" N THR A 20 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 39 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR A 60 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA A 115 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN A 62 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A 117 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN A 64 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N SER A 119 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.750A pdb=" N GLY A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR A 156 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 175 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP A 176 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A 191 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 178 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 189 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 180 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N GLU A 190 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N ASP A 508 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N GLU A 192 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N GLN A 506 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N GLN A 194 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA A 504 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 496 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 505 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 494 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET A 507 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP A 492 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 331 removed outlier: 3.542A pdb=" N GLY A 339 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN A 349 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 432 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU A 433 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 625 through 633 removed outlier: 6.930A pdb=" N PHE A 638 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 632 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N GLU A 646 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N LEU A 687 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 648 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG A 686 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 627 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.254A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR B 60 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA B 115 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN B 62 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 117 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN B 64 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N SER B 119 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.748A pdb=" N GLY B 181 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 156 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B 175 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP B 176 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 191 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 189 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA B 180 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N GLU B 190 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASP B 508 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU B 192 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N GLN B 506 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N GLN B 194 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA B 504 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 496 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 505 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS B 494 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET B 507 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B 492 " --> pdb=" O MET B 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 331 removed outlier: 3.541A pdb=" N GLY B 339 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN B 349 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 432 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU B 433 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 363 through 365 Processing sheet with id=AB2, first strand: chain 'B' and resid 557 through 559 removed outlier: 6.707A pdb=" N THR B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 625 through 632 removed outlier: 11.225A pdb=" N GLY B 627 " --> pdb=" O GLY B 642 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N GLY B 642 " --> pdb=" O GLY B 627 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 629 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 640 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 631 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 641 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU B 687 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 648 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 678 " --> pdb=" O ARG B 686 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER B 688 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL B 676 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.614A pdb=" N THR C 20 " --> pdb=" O ILE C 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.614A pdb=" N THR C 20 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA C 39 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR C 60 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA C 115 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN C 62 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 117 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN C 64 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N SER C 119 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.750A pdb=" N GLY C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR C 156 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU C 175 " --> pdb=" O TYR C 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP C 176 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 191 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 178 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 189 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 180 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N GLU C 190 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N ASP C 508 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU C 192 " --> pdb=" O GLN C 506 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N GLN C 506 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N GLN C 194 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA C 504 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY C 501 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA C 496 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU C 505 " --> pdb=" O LYS C 494 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS C 494 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET C 507 " --> pdb=" O ASP C 492 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP C 492 " --> pdb=" O MET C 507 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 327 through 331 removed outlier: 3.542A pdb=" N GLY C 339 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU C 347 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C 434 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN C 349 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 432 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 363 through 365 Processing sheet with id=AB9, first strand: chain 'C' and resid 554 through 559 removed outlier: 3.654A pdb=" N ALA C 599 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 598 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 586 " --> pdb=" O ALA C 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 624 through 633 removed outlier: 10.009A pdb=" N THR C 626 " --> pdb=" O GLY C 642 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY C 642 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 628 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 638 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE C 632 " --> pdb=" O GLY C 636 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY C 636 " --> pdb=" O ILE C 632 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE C 641 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE C 685 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 687 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS C 650 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER C 688 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL C 676 " --> pdb=" O SER C 688 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 2091 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: 5.60 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2601 1.28 - 1.42: 3240 1.42 - 1.55: 9000 1.55 - 1.69: 5 1.69 - 1.83: 115 Bond restraints: 14961 Sorted by residual: bond pdb=" C ARG C 325 " pdb=" O ARG C 325 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.07e-02 8.73e+03 5.22e+01 bond pdb=" C THR A 15 " pdb=" O THR A 15 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.14e-02 7.69e+03 5.11e+01 bond pdb=" C ARG B 399 " pdb=" O ARG B 399 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.25e-02 6.40e+03 5.11e+01 bond pdb=" C PRO A 314 " pdb=" O PRO A 314 " ideal model delta sigma weight residual 1.233 1.150 0.083 1.16e-02 7.43e+03 5.08e+01 bond pdb=" C THR C 348 " pdb=" O THR C 348 " ideal model delta sigma weight residual 1.233 1.152 0.082 1.15e-02 7.56e+03 5.04e+01 ... (remaining 14956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 17653 2.82 - 5.64: 2470 5.64 - 8.46: 221 8.46 - 11.28: 35 11.28 - 14.10: 4 Bond angle restraints: 20383 Sorted by residual: angle pdb=" N GLU B 485 " pdb=" CA GLU B 485 " pdb=" C GLU B 485 " ideal model delta sigma weight residual 112.59 98.49 14.10 1.22e+00 6.72e-01 1.34e+02 angle pdb=" N PHE C 551 " pdb=" CA PHE C 551 " pdb=" C PHE C 551 " ideal model delta sigma weight residual 112.59 98.51 14.08 1.22e+00 6.72e-01 1.33e+02 angle pdb=" N ARG C 399 " pdb=" CA ARG C 399 " pdb=" C ARG C 399 " ideal model delta sigma weight residual 111.11 99.42 11.69 1.20e+00 6.94e-01 9.50e+01 angle pdb=" N ILE A 273 " pdb=" CA ILE A 273 " pdb=" C ILE A 273 " ideal model delta sigma weight residual 110.62 101.78 8.84 1.02e+00 9.61e-01 7.52e+01 angle pdb=" N ILE B 273 " pdb=" CA ILE B 273 " pdb=" C ILE B 273 " ideal model delta sigma weight residual 110.62 101.78 8.84 1.02e+00 9.61e-01 7.51e+01 ... (remaining 20378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8311 17.92 - 35.84: 567 35.84 - 53.76: 131 53.76 - 71.68: 19 71.68 - 89.60: 10 Dihedral angle restraints: 9038 sinusoidal: 3143 harmonic: 5895 Sorted by residual: dihedral pdb=" C ILE C 401 " pdb=" N ILE C 401 " pdb=" CA ILE C 401 " pdb=" CB ILE C 401 " ideal model delta harmonic sigma weight residual -122.00 -141.40 19.40 0 2.50e+00 1.60e-01 6.02e+01 dihedral pdb=" C ILE B 401 " pdb=" N ILE B 401 " pdb=" CA ILE B 401 " pdb=" CB ILE B 401 " ideal model delta harmonic sigma weight residual -122.00 -141.39 19.39 0 2.50e+00 1.60e-01 6.02e+01 dihedral pdb=" C ILE A 401 " pdb=" N ILE A 401 " pdb=" CA ILE A 401 " pdb=" CB ILE A 401 " ideal model delta harmonic sigma weight residual -122.00 -141.38 19.38 0 2.50e+00 1.60e-01 6.01e+01 ... (remaining 9035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1886 0.127 - 0.254: 521 0.254 - 0.380: 70 0.380 - 0.507: 4 0.507 - 0.634: 3 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 1.80 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA ILE B 401 " pdb=" N ILE B 401 " pdb=" C ILE B 401 " pdb=" CB ILE B 401 " both_signs ideal model delta sigma weight residual False 2.43 1.80 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA ILE C 401 " pdb=" N ILE C 401 " pdb=" C ILE C 401 " pdb=" CB ILE C 401 " both_signs ideal model delta sigma weight residual False 2.43 1.80 0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 2481 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 128 " 0.026 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C ILE C 128 " -0.089 2.00e-02 2.50e+03 pdb=" O ILE C 128 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL C 129 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 128 " 0.025 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C ILE B 128 " -0.089 2.00e-02 2.50e+03 pdb=" O ILE B 128 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL B 129 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 16 " 0.023 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C VAL B 16 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL B 16 " 0.032 2.00e-02 2.50e+03 pdb=" N THR B 17 " 0.028 2.00e-02 2.50e+03 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 308 2.65 - 3.21: 13394 3.21 - 3.77: 21001 3.77 - 4.34: 28762 4.34 - 4.90: 46933 Nonbonded interactions: 110398 Sorted by model distance: nonbonded pdb=" O ASP C 492 " pdb=" OD1 ASP C 492 " model vdw 2.082 3.040 nonbonded pdb=" O ASP A 492 " pdb=" OD1 ASP A 492 " model vdw 2.083 3.040 nonbonded pdb=" O ASP B 492 " pdb=" OD1 ASP B 492 " model vdw 2.083 3.040 nonbonded pdb=" O LYS A 321 " pdb=" OD1 ASP A 322 " model vdw 2.107 3.040 nonbonded pdb=" OD1 ASP A 486 " pdb=" N HIS A 487 " model vdw 2.206 3.120 ... (remaining 110393 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 1 through 35 or (resid 36 through 37 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 291 or (resid 292 throug \ h 293 and (name N or name CA or name C or name O or name CB )) or resid 294 thro \ ugh 318 or (resid 319 through 323 and (name N or name CA or name C or name O or \ name CB )) or resid 324 through 402 or (resid 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 through 434 or (resid 435 and (name N or \ name CA or name C or name O or name CB )) or resid 436 through 546 or (resid 54 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 548 through \ 549 or (resid 550 and (name N or name CA or name C or name O or name CB )) or re \ sid 551 through 553 or (resid 554 and (name N or name CA or name C or name O or \ name CB )) or resid 555 through 560 or (resid 561 and (name N or name CA or name \ C or name O or name CB )) or resid 562 or (resid 563 through 564 and (name N or \ name CA or name C or name O or name CB )) or resid 565 through 566 or (resid 56 \ 7 through 569 and (name N or name CA or name C or name O or name CB )) or resid \ 570 through 595 or (resid 596 and (name N or name CA or name C or name O or name \ CB )) or resid 597 through 600 or (resid 601 and (name N or name CA or name C o \ r name O or name CB )) or resid 602 or (resid 603 through 608 and (name N or nam \ e CA or name C or name O or name CB )) or resid 609 through 689)) selection = (chain 'B' and (resid 1 through 291 or (resid 292 through 293 and (name N or nam \ e CA or name C or name O or name CB )) or resid 294 through 402 or (resid 403 an \ d (name N or name CA or name C or name O or name CB )) or resid 404 through 434 \ or (resid 435 and (name N or name CA or name C or name O or name CB )) or resid \ 436 through 549 or (resid 550 and (name N or name CA or name C or name O or name \ CB )) or resid 551 through 556 or (resid 557 through 559 and (name N or name CA \ or name C or name O or name CB )) or resid 560 through 567 or (resid 568 throug \ h 569 and (name N or name CA or name C or name O or name CB )) or resid 570 or ( \ resid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 \ through 588 or (resid 589 through 592 and (name N or name CA or name C or name O \ or name CB )) or resid 593 through 618 or (resid 619 through 621 and (name N or \ name CA or name C or name O or name CB )) or (resid 622 through 626 and (name N \ or name CA or name C or name O or name CB )) or (resid 627 through 635 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 636 through 641 and ( \ name N or name CA or name C or name O or name CB )) or (resid 642 through 668 an \ d (name N or name CA or name C or name O or name CB )) or (resid 669 through 672 \ and (name N or name CA or name C or name O or name CB )) or resid 673 or (resid \ 674 through 682 and (name N or name CA or name C or name O or name CB )) or (re \ sid 683 through 689 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 1 through 318 or (resid 319 through 323 and (name N or nam \ e CA or name C or name O or name CB )) or resid 324 through 553 or (resid 554 an \ d (name N or name CA or name C or name O or name CB )) or resid 555 through 556 \ or (resid 557 through 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 588 or (resid 589 through 592 and (name N or name CA or \ name C or name O or name CB )) or resid 593 through 618 or (resid 619 through 62 \ 1 and (name N or name CA or name C or name O or name CB )) or (resid 622 through \ 626 and (name N or name CA or name C or name O or name CB )) or (resid 627 thro \ ugh 635 and (name N or name CA or name C or name O or name CB )) or (resid 636 t \ hrough 641 and (name N or name CA or name C or name O or name CB )) or (resid 64 \ 2 through 668 and (name N or name CA or name C or name O or name CB )) or (resid \ 669 through 672 and (name N or name CA or name C or name O or name CB )) or res \ id 673 or (resid 674 through 682 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 683 through 689 and (name N or name CA or name C or name O o \ r name CB )))) } 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=0.50 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: 0.820 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.790 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.016 0.089 14961 Z= 1.053 Angle : 1.972 14.099 20383 Z= 1.441 Chirality : 0.116 0.634 2484 Planarity : 0.010 0.052 2692 Dihedral : 13.712 89.601 5252 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 1.70 % Allowed : 6.53 % Favored : 91.77 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2073 helix: -1.34 (0.18), residues: 611 sheet: 0.55 (0.24), residues: 411 loop : -0.91 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.007 TRP C 233 HIS 0.013 0.003 HIS A 14 PHE 0.031 0.008 PHE C 343 TYR 0.034 0.008 TYR C 380 ARG 0.012 0.002 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 357 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: A 3 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.6821 (p0) REVERT: A 74 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.7924 (Cg_endo) REVERT: A 174 LYS cc_start: 0.8090 (ptpt) cc_final: 0.7723 (ptpt) REVERT: A 243 ASN cc_start: 0.6610 (t0) cc_final: 0.5884 (m110) REVERT: A 302 LYS cc_start: 0.7281 (mtmt) cc_final: 0.6890 (mttp) REVERT: A 418 MET cc_start: 0.6002 (mmm) cc_final: 0.5599 (mmp) REVERT: A 507 MET cc_start: 0.8218 (mtt) cc_final: 0.7953 (mtp) REVERT: B 1 MET cc_start: 0.4691 (ttp) cc_final: 0.4398 (ttm) REVERT: B 15 THR cc_start: 0.8941 (t) cc_final: 0.8546 (m) REVERT: B 86 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7409 (tt0) REVERT: B 128 ILE cc_start: 0.8706 (pp) cc_final: 0.8280 (mm) REVERT: B 315 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.5958 (mtm110) REVERT: B 389 GLU cc_start: 0.7238 (mt-10) cc_final: 0.5845 (mm-30) REVERT: B 537 MET cc_start: 0.8181 (mtp) cc_final: 0.7711 (mtm) REVERT: B 539 GLN cc_start: 0.7335 (tt0) cc_final: 0.7001 (mt0) REVERT: C 389 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6423 (mm-30) REVERT: C 451 MET cc_start: 0.7404 (mtt) cc_final: 0.7190 (mtt) REVERT: C 510 LYS cc_start: 0.7529 (mttm) cc_final: 0.7156 (mtmt) outliers start: 24 outliers final: 3 residues processed: 373 average time/residue: 0.3334 time to fit residues: 171.0496 Evaluate side-chains 181 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 548 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 234 GLN A 298 HIS A 381 ASN A 525 GLN B 64 GLN B 121 ASN B 146 ASN B 212 GLN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 520 GLN C 64 GLN C 146 ASN C 160 GLN C 200 GLN C 381 ASN C 542 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14961 Z= 0.215 Angle : 0.622 6.693 20383 Z= 0.345 Chirality : 0.048 0.181 2484 Planarity : 0.004 0.047 2692 Dihedral : 5.634 56.797 2213 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.13 % Allowed : 10.65 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2073 helix: 0.80 (0.20), residues: 630 sheet: 0.78 (0.23), residues: 496 loop : -0.70 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 233 HIS 0.004 0.001 HIS C 14 PHE 0.020 0.002 PHE A 145 TYR 0.024 0.002 TYR B 385 ARG 0.006 0.001 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.627 Fit side-chains REVERT: A 3 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.6940 (p0) REVERT: A 51 LYS cc_start: 0.5280 (tttm) cc_final: 0.4763 (mttt) REVERT: A 243 ASN cc_start: 0.6404 (t0) cc_final: 0.5757 (m-40) REVERT: B 1 MET cc_start: 0.4496 (ttp) cc_final: 0.4162 (ttm) REVERT: B 15 THR cc_start: 0.8709 (t) cc_final: 0.8450 (m) REVERT: B 128 ILE cc_start: 0.8577 (pp) cc_final: 0.8238 (mm) REVERT: B 259 ARG cc_start: 0.6995 (mtt90) cc_final: 0.6345 (mmm160) REVERT: B 389 GLU cc_start: 0.7434 (mt-10) cc_final: 0.5893 (mm-30) REVERT: B 418 MET cc_start: 0.7954 (tpt) cc_final: 0.7590 (tpp) REVERT: B 537 MET cc_start: 0.8026 (mtp) cc_final: 0.7556 (mtm) REVERT: C 276 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: C 280 THR cc_start: 0.6107 (m) cc_final: 0.5801 (t) REVERT: C 347 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7509 (pm20) REVERT: C 389 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6586 (mm-30) REVERT: C 430 GLU cc_start: 0.8064 (mp0) cc_final: 0.7658 (mt-10) REVERT: C 510 LYS cc_start: 0.7495 (mttm) cc_final: 0.7083 (mtmt) outliers start: 30 outliers final: 13 residues processed: 211 average time/residue: 0.2749 time to fit residues: 86.4543 Evaluate side-chains 167 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 548 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 202 optimal weight: 50.0000 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 63 optimal weight: 50.0000 chunk 150 optimal weight: 3.9990 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 158 ASN A 211 GLN A 298 HIS ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 474 ASN C 209 HIS C 212 GLN C 520 GLN C 524 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 14961 Z= 0.452 Angle : 0.700 7.647 20383 Z= 0.373 Chirality : 0.052 0.193 2484 Planarity : 0.005 0.054 2692 Dihedral : 5.579 58.758 2208 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.48 % Allowed : 13.13 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2073 helix: 1.05 (0.20), residues: 630 sheet: 0.51 (0.23), residues: 499 loop : -0.95 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 233 HIS 0.009 0.002 HIS C 379 PHE 0.020 0.003 PHE A 145 TYR 0.028 0.003 TYR A 258 ARG 0.005 0.001 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 1.688 Fit side-chains REVERT: A 243 ASN cc_start: 0.6482 (t0) cc_final: 0.5849 (m-40) REVERT: A 253 ARG cc_start: 0.6666 (mtm-85) cc_final: 0.6434 (ttm170) REVERT: A 344 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8757 (m) REVERT: B 1 MET cc_start: 0.4896 (ttp) cc_final: 0.4393 (ttm) REVERT: B 128 ILE cc_start: 0.8606 (pp) cc_final: 0.8243 (mm) REVERT: B 249 LEU cc_start: 0.6222 (mt) cc_final: 0.5950 (tt) REVERT: B 259 ARG cc_start: 0.7185 (mtt90) cc_final: 0.6630 (mtp180) REVERT: B 372 ARG cc_start: 0.6651 (ttp-110) cc_final: 0.5539 (mtp180) REVERT: B 418 MET cc_start: 0.8176 (tpt) cc_final: 0.7830 (tpt) REVERT: B 508 ASP cc_start: 0.7646 (t0) cc_final: 0.7292 (m-30) REVERT: B 538 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 276 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: C 389 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6617 (mm-30) outliers start: 49 outliers final: 26 residues processed: 205 average time/residue: 0.2696 time to fit residues: 83.4125 Evaluate side-chains 176 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 435 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS B 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14961 Z= 0.199 Angle : 0.524 5.551 20383 Z= 0.281 Chirality : 0.045 0.169 2484 Planarity : 0.004 0.046 2692 Dihedral : 4.661 31.221 2204 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.56 % Allowed : 15.26 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 2073 helix: 1.57 (0.20), residues: 634 sheet: 0.62 (0.24), residues: 511 loop : -0.80 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 233 HIS 0.003 0.001 HIS A 532 PHE 0.014 0.001 PHE C 78 TYR 0.014 0.002 TYR C 380 ARG 0.002 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.705 Fit side-chains REVERT: A 51 LYS cc_start: 0.6391 (tttm) cc_final: 0.5693 (mttp) REVERT: A 138 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (mm) REVERT: A 243 ASN cc_start: 0.6531 (t0) cc_final: 0.5907 (m-40) REVERT: A 253 ARG cc_start: 0.6844 (mtm-85) cc_final: 0.6615 (ttm170) REVERT: A 418 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6491 (mmm) REVERT: B 1 MET cc_start: 0.4959 (ttp) cc_final: 0.4393 (ttm) REVERT: B 128 ILE cc_start: 0.8410 (pp) cc_final: 0.8190 (mm) REVERT: B 249 LEU cc_start: 0.6218 (mt) cc_final: 0.5991 (tt) REVERT: B 259 ARG cc_start: 0.7174 (mtt90) cc_final: 0.6685 (mtp180) REVERT: B 418 MET cc_start: 0.8275 (tpt) cc_final: 0.7777 (tpt) REVERT: B 420 LYS cc_start: 0.6806 (ttpt) cc_final: 0.5921 (tptt) REVERT: B 508 ASP cc_start: 0.7414 (t0) cc_final: 0.7126 (m-30) REVERT: B 538 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 389 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6594 (mm-30) REVERT: C 491 MET cc_start: 0.7988 (ttm) cc_final: 0.7761 (ttm) REVERT: C 597 ILE cc_start: 0.0986 (OUTLIER) cc_final: 0.0435 (mt) outliers start: 36 outliers final: 18 residues processed: 183 average time/residue: 0.2509 time to fit residues: 70.2187 Evaluate side-chains 162 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS B 211 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14961 Z= 0.203 Angle : 0.508 4.913 20383 Z= 0.271 Chirality : 0.045 0.165 2484 Planarity : 0.004 0.046 2692 Dihedral : 4.408 23.016 2203 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.70 % Allowed : 15.90 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2073 helix: 1.68 (0.20), residues: 643 sheet: 0.68 (0.24), residues: 509 loop : -0.77 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS C 379 PHE 0.013 0.001 PHE A 145 TYR 0.016 0.002 TYR C 380 ARG 0.002 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 1.709 Fit side-chains REVERT: A 51 LYS cc_start: 0.6442 (tttm) cc_final: 0.5742 (mttp) REVERT: A 243 ASN cc_start: 0.6542 (t0) cc_final: 0.5834 (m-40) REVERT: A 253 ARG cc_start: 0.6921 (mtm-85) cc_final: 0.6609 (ttm170) REVERT: A 418 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6502 (mmm) REVERT: B 162 VAL cc_start: 0.8702 (p) cc_final: 0.8427 (m) REVERT: B 259 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6788 (mtt-85) REVERT: B 418 MET cc_start: 0.8317 (tpt) cc_final: 0.7823 (tpt) REVERT: B 420 LYS cc_start: 0.6687 (ttpt) cc_final: 0.5863 (tptt) REVERT: B 508 ASP cc_start: 0.7560 (t0) cc_final: 0.7259 (m-30) REVERT: B 538 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7383 (tm-30) REVERT: C 389 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6696 (mm-30) REVERT: C 491 MET cc_start: 0.8013 (ttm) cc_final: 0.7733 (ttm) REVERT: C 597 ILE cc_start: 0.1059 (OUTLIER) cc_final: 0.0463 (mt) outliers start: 38 outliers final: 28 residues processed: 172 average time/residue: 0.2554 time to fit residues: 67.4465 Evaluate side-chains 171 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 50.0000 chunk 179 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 199 optimal weight: 40.0000 chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 50.0000 chunk 104 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 14961 Z= 0.701 Angle : 0.818 11.063 20383 Z= 0.427 Chirality : 0.056 0.313 2484 Planarity : 0.006 0.058 2692 Dihedral : 5.556 28.940 2203 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.90 % Allowed : 16.32 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2073 helix: 0.55 (0.20), residues: 645 sheet: 0.08 (0.23), residues: 500 loop : -1.27 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 233 HIS 0.011 0.002 HIS C 379 PHE 0.020 0.003 PHE C 207 TYR 0.035 0.003 TYR C 380 ARG 0.009 0.001 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 1.603 Fit side-chains REVERT: A 51 LYS cc_start: 0.6477 (tttm) cc_final: 0.5793 (mttp) REVERT: A 243 ASN cc_start: 0.6474 (t0) cc_final: 0.6122 (m-40) REVERT: A 418 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7050 (mmm) REVERT: B 259 ARG cc_start: 0.7412 (mtt90) cc_final: 0.6850 (mtt-85) REVERT: B 372 ARG cc_start: 0.6788 (ttp-110) cc_final: 0.5590 (mtp180) REVERT: B 418 MET cc_start: 0.8428 (tpt) cc_final: 0.7942 (tpt) REVERT: B 508 ASP cc_start: 0.7613 (t0) cc_final: 0.7400 (m-30) REVERT: B 538 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 276 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5784 (tm-30) REVERT: C 440 MET cc_start: 0.8700 (mmt) cc_final: 0.8195 (mmt) REVERT: C 597 ILE cc_start: 0.1286 (OUTLIER) cc_final: 0.0822 (mt) outliers start: 55 outliers final: 35 residues processed: 181 average time/residue: 0.2461 time to fit residues: 68.1035 Evaluate side-chains 174 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14961 Z= 0.189 Angle : 0.528 8.944 20383 Z= 0.277 Chirality : 0.044 0.151 2484 Planarity : 0.004 0.045 2692 Dihedral : 4.609 25.859 2203 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.56 % Allowed : 18.24 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2073 helix: 1.37 (0.20), residues: 640 sheet: 0.47 (0.24), residues: 499 loop : -0.97 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 233 HIS 0.003 0.001 HIS C 14 PHE 0.015 0.001 PHE C 78 TYR 0.014 0.002 TYR B 380 ARG 0.004 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 2.313 Fit side-chains REVERT: A 51 LYS cc_start: 0.6760 (tttm) cc_final: 0.6061 (mttp) REVERT: A 243 ASN cc_start: 0.6472 (t0) cc_final: 0.6235 (m-40) REVERT: A 418 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6914 (mmm) REVERT: A 466 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7079 (mmm) REVERT: C 276 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5779 (tm-30) REVERT: C 484 ASP cc_start: 0.7888 (p0) cc_final: 0.7681 (p0) REVERT: C 597 ILE cc_start: 0.1020 (OUTLIER) cc_final: 0.0558 (mt) outliers start: 36 outliers final: 26 residues processed: 170 average time/residue: 0.2792 time to fit residues: 72.8880 Evaluate side-chains 165 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 0.0770 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 126 optimal weight: 30.0000 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14961 Z= 0.205 Angle : 0.524 7.879 20383 Z= 0.274 Chirality : 0.045 0.148 2484 Planarity : 0.004 0.046 2692 Dihedral : 4.358 24.908 2203 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.77 % Allowed : 18.17 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 2073 helix: 1.60 (0.21), residues: 641 sheet: 0.67 (0.24), residues: 484 loop : -0.96 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 233 HIS 0.003 0.001 HIS C 14 PHE 0.014 0.001 PHE C 78 TYR 0.016 0.002 TYR C 380 ARG 0.003 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.534 Fit side-chains REVERT: A 51 LYS cc_start: 0.6707 (tttm) cc_final: 0.6018 (mttp) REVERT: A 243 ASN cc_start: 0.6587 (t0) cc_final: 0.6379 (m-40) REVERT: A 367 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6922 (mt-10) REVERT: A 418 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6965 (mmm) REVERT: A 466 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7126 (mmm) REVERT: B 259 ARG cc_start: 0.7141 (mtt90) cc_final: 0.6627 (mtp180) REVERT: B 538 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7002 (tp30) REVERT: C 198 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6258 (pm20) REVERT: C 276 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5785 (tm-30) REVERT: C 440 MET cc_start: 0.8489 (mmt) cc_final: 0.8039 (mmt) REVERT: C 597 ILE cc_start: 0.1028 (OUTLIER) cc_final: 0.0584 (mt) outliers start: 39 outliers final: 26 residues processed: 170 average time/residue: 0.2616 time to fit residues: 67.5979 Evaluate side-chains 170 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14961 Z= 0.234 Angle : 0.533 11.378 20383 Z= 0.278 Chirality : 0.045 0.194 2484 Planarity : 0.004 0.046 2692 Dihedral : 4.329 25.141 2203 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.41 % Allowed : 18.74 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2073 helix: 1.70 (0.20), residues: 641 sheet: 0.65 (0.24), residues: 486 loop : -0.95 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 233 HIS 0.004 0.001 HIS C 379 PHE 0.013 0.002 PHE C 78 TYR 0.018 0.002 TYR C 380 ARG 0.003 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.538 Fit side-chains REVERT: A 51 LYS cc_start: 0.6687 (tttm) cc_final: 0.6042 (mttp) REVERT: A 367 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 418 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7083 (mmm) REVERT: A 466 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7075 (mmm) REVERT: B 162 VAL cc_start: 0.8682 (p) cc_final: 0.8439 (m) REVERT: B 259 ARG cc_start: 0.7144 (mtt90) cc_final: 0.6662 (mtp180) REVERT: B 538 GLU cc_start: 0.7884 (tm-30) cc_final: 0.6998 (tp30) REVERT: C 198 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6215 (pm20) REVERT: C 276 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5883 (tm-30) REVERT: C 597 ILE cc_start: 0.1096 (OUTLIER) cc_final: 0.0649 (mt) outliers start: 34 outliers final: 26 residues processed: 165 average time/residue: 0.2599 time to fit residues: 65.0849 Evaluate side-chains 163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 3.9990 chunk 195 optimal weight: 0.0980 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 205 optimal weight: 50.0000 chunk 188 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS B 211 GLN C 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14961 Z= 0.257 Angle : 0.543 12.183 20383 Z= 0.282 Chirality : 0.045 0.149 2484 Planarity : 0.004 0.047 2692 Dihedral : 4.346 25.314 2203 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.56 % Allowed : 18.52 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 2073 helix: 1.69 (0.20), residues: 642 sheet: 0.63 (0.24), residues: 488 loop : -0.98 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 233 HIS 0.006 0.001 HIS B 403 PHE 0.013 0.002 PHE C 78 TYR 0.019 0.002 TYR C 380 ARG 0.004 0.000 ARG B 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.667 Fit side-chains REVERT: A 51 LYS cc_start: 0.6683 (tttm) cc_final: 0.6044 (mttp) REVERT: A 367 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6865 (mt-10) REVERT: A 415 MET cc_start: 0.9428 (mmp) cc_final: 0.9133 (mmm) REVERT: A 418 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7072 (mmm) REVERT: A 466 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7120 (mmm) REVERT: B 162 VAL cc_start: 0.8691 (p) cc_final: 0.8449 (m) REVERT: B 259 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6651 (mtt-85) REVERT: B 538 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7014 (tp30) REVERT: C 198 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: C 276 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5887 (tm-30) outliers start: 36 outliers final: 29 residues processed: 158 average time/residue: 0.2455 time to fit residues: 59.6054 Evaluate side-chains 165 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.0070 chunk 174 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.178760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138657 restraints weight = 17372.149| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.98 r_work: 0.3270 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14961 Z= 0.187 Angle : 0.503 12.136 20383 Z= 0.262 Chirality : 0.044 0.147 2484 Planarity : 0.004 0.046 2692 Dihedral : 4.110 24.008 2203 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.41 % Allowed : 18.81 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2073 helix: 1.94 (0.20), residues: 641 sheet: 0.83 (0.25), residues: 470 loop : -0.93 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 233 HIS 0.006 0.001 HIS B 403 PHE 0.014 0.001 PHE C 78 TYR 0.014 0.001 TYR C 380 ARG 0.002 0.000 ARG A 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.59 seconds wall clock time: 55 minutes 7.81 seconds (3307.81 seconds total)