Starting phenix.real_space_refine on Sat Sep 12 08:41:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.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 { model { file = "/net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ogk_12882/09_2026/7ogk_12882.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.084 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 62 5.16 5 C 9155 2.51 5 N 2647 2.21 5 O 2859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14731 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4947 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 695, 4941 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 22, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 9, 'TYR:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 223 Conformer: "B" Number of residues, atoms: 695, 4941 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 22, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 9, 'TYR:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 223 bond proxies already assigned to first conformer: 5003 Chain: "B" Number of atoms: 4798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 4798 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 397 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ARG:plan': 14, 'GLU:plan': 31, 'ASN:plan1': 3, 'ASP:plan': 14, 'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 305 Chain: "C" Number of atoms: 4847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 4847 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 28, 'TRANS': 666} Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLU:plan': 27, 'ASN:plan1': 3, 'ARG:plan': 10, 'GLN:plan1': 6, 'ASP:plan': 12, 'PHE:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 264 Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 122 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 3} Link IDs: {'rna2p': 5, 'rna3p': 2} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {' A%rna2p_pur:plan': 5, ' A%rna2p_pur:plan2': 5, ' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.16, per 1000 atoms: 0.28 Number of scatterers: 14731 At special positions: 0 Unit cell: (112.89, 110.76, 145.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 8 15.00 O 2859 8.00 N 2647 7.00 C 9155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 880.4 milliseconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 21 sheets defined 37.1% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.602A 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 125 through 141 removed outlier: 4.571A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.613A pdb=" N LYS A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 258 removed outlier: 3.885A pdb=" N ARG A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 289 through 310 removed outlier: 3.886A pdb=" N LEU A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.716A pdb=" N VAL A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.964A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.733A pdb=" N ALA A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 removed outlier: 4.434A pdb=" N HIS A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 541 removed outlier: 3.949A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.749A pdb=" N VAL A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 569 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 564 through 570' Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 601 through 616 Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'B' and resid 85 through 103 removed outlier: 3.919A pdb=" N ILE B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Proline residue: B 98 - end of helix Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 125 through 141 removed outlier: 4.406A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.969A pdb=" N GLU B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.514A pdb=" N VAL B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.559A pdb=" N ASP B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.747A pdb=" N LEU B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 312 removed outlier: 3.598A pdb=" N LEU B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 397 through 413 removed outlier: 4.138A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 437 through 454 removed outlier: 3.727A pdb=" N ALA B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 487 removed outlier: 3.914A pdb=" N HIS B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 541 removed outlier: 4.111A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 536 " --> pdb=" O HIS B 532 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 541 " --> pdb=" O MET B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.526A pdb=" N GLY B 570 " --> pdb=" O LYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 584 removed outlier: 3.579A pdb=" N LEU B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 617 removed outlier: 3.557A pdb=" N ILE B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 85 through 100 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: 3.728A pdb=" N ILE C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 160 Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.669A pdb=" N GLU C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 removed outlier: 4.146A pdb=" N GLU C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 260 removed outlier: 3.989A pdb=" N LEU C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 280 Processing helix chain 'C' and resid 289 through 312 removed outlier: 3.715A pdb=" N ILE C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.747A pdb=" N VAL C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 413 removed outlier: 4.131A pdb=" N ALA C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 3.686A pdb=" N ALA C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.575A pdb=" N MET C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 522 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 570 through 573 Processing helix chain 'C' and resid 574 through 584 removed outlier: 3.512A pdb=" N ALA C 578 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.561A pdb=" N GLU C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.642A pdb=" N VAL A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA A 39 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 60 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA A 115 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 62 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 117 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN A 64 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 8.330A 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: 5.613A pdb=" N LEU A 187 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 505 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER A 503 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU A 195 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY A 501 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA A 496 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 505 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 494 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET A 507 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 7.032A 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: 6.512A pdb=" N GLN A 349 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 8.326A 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 555 through 559 Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.948A pdb=" N GLY A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A 632 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE A 638 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 688 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG A 686 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 11 removed outlier: 6.434A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR B 60 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA B 115 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN B 62 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL B 117 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLN B 64 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 8.444A 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: 3.564A pdb=" N GLY B 150 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N GLU B 190 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N ASP B 508 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N GLU B 192 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N GLN B 506 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N GLN B 194 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N ALA B 504 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 496 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B 505 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS B 494 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N MET B 507 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 7.103A 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: 6.300A pdb=" N GLN B 349 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 8.050A 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 366 removed outlier: 3.851A pdb=" N GLN B 363 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP B 374 " --> pdb=" O GLN B 363 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 554 through 559 Processing sheet with id=AB3, first strand: chain 'B' and resid 629 through 633 removed outlier: 6.412A pdb=" N PHE B 638 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE B 632 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 675 through 676 removed outlier: 4.312A pdb=" N SER B 688 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 11 removed outlier: 6.487A pdb=" N ALA C 39 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 60 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA C 115 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN C 62 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL C 117 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN C 64 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N SER C 119 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 162 through 163 removed outlier: 5.568A pdb=" N LEU C 187 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 505 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER C 503 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 498 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 162 through 163 removed outlier: 5.568A pdb=" N LEU C 187 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 505 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER C 503 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 498 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 328 through 331 removed outlier: 6.379A pdb=" N GLN C 349 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 363 through 365 Processing sheet with id=AC1, first strand: chain 'C' and resid 554 through 559 removed outlier: 3.700A pdb=" N ALA C 598 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 586 " --> pdb=" O ALA C 598 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 638 through 640 removed outlier: 6.791A pdb=" N PHE C 638 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 680 through 681 782 hydrogen bonds defined for protein. 2112 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2573 1.31 - 1.44: 3480 1.44 - 1.57: 8740 1.57 - 1.70: 17 1.70 - 1.83: 121 Bond restraints: 14931 Sorted by residual: bond pdb=" C LYS A 228 " pdb=" O LYS A 228 " ideal model delta sigma weight residual 1.235 1.421 -0.186 1.28e-02 6.10e+03 2.12e+02 bond pdb=" N ARG B 83 " pdb=" CA ARG B 83 " ideal model delta sigma weight residual 1.453 1.494 -0.041 8.30e-03 1.45e+04 2.48e+01 bond pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 2.06e+01 bond pdb=" N ILE B 654 " pdb=" CA ILE B 654 " ideal model delta sigma weight residual 1.460 1.498 -0.037 8.60e-03 1.35e+04 1.88e+01 bond pdb=" CA SER C 429 " pdb=" CB SER C 429 " ideal model delta sigma weight residual 1.528 1.469 0.058 1.39e-02 5.18e+03 1.74e+01 ... (remaining 14926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 18569 2.97 - 5.94: 1736 5.94 - 8.91: 50 8.91 - 11.88: 2 11.88 - 14.85: 4 Bond angle restraints: 20361 Sorted by residual: angle pdb=" O LYS A 228 " pdb=" C LYS A 228 " pdb=" CA ALYS A 228 " ideal model delta sigma weight residual 120.69 132.80 -12.11 1.13e+00 7.83e-01 1.15e+02 angle pdb=" N LYS A 228 " pdb=" CA BLYS A 228 " pdb=" C LYS A 228 " ideal model delta sigma weight residual 109.84 124.69 -14.85 1.39e+00 5.18e-01 1.14e+02 angle pdb=" O LYS A 228 " pdb=" C LYS A 228 " pdb=" CA BLYS A 228 " ideal model delta sigma weight residual 120.69 132.70 -12.01 1.13e+00 7.83e-01 1.13e+02 angle pdb=" N LYS A 228 " pdb=" CA ALYS A 228 " pdb=" C LYS A 228 " ideal model delta sigma weight residual 109.84 124.60 -14.76 1.39e+00 5.18e-01 1.13e+02 angle pdb=" O LYS A 228 " pdb=" C LYS A 228 " pdb=" N PRO A 229 " ideal model delta sigma weight residual 121.43 111.45 9.98 1.12e+00 7.97e-01 7.94e+01 ... (remaining 20356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8344 17.79 - 35.57: 492 35.57 - 53.36: 127 53.36 - 71.15: 36 71.15 - 88.93: 25 Dihedral angle restraints: 9024 sinusoidal: 3107 harmonic: 5917 Sorted by residual: dihedral pdb=" C4' A D 6 " pdb=" C3' A D 6 " pdb=" C2' A D 6 " pdb=" C1' A D 6 " ideal model delta sinusoidal sigma weight residual 36.35 -36.43 72.78 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' A D 2 " pdb=" C3' A D 2 " pdb=" C2' A D 2 " pdb=" C1' A D 2 " ideal model delta sinusoidal sigma weight residual 36.34 -36.37 72.71 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' A D 5 " pdb=" C3' A D 5 " pdb=" C2' A D 5 " pdb=" C1' A D 5 " ideal model delta sinusoidal sigma weight residual 36.34 -35.58 71.92 1 3.10e+00 1.04e-01 6.89e+02 ... (remaining 9021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 2045 0.150 - 0.300: 407 0.300 - 0.450: 4 0.450 - 0.600: 0 0.600 - 0.750: 1 Chirality restraints: 2457 Sorted by residual: chirality pdb=" P A D 1 " pdb=" OP1 A D 1 " pdb=" OP2 A D 1 " pdb=" O5' A D 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.92 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CA ASN A 381 " pdb=" N ASN A 381 " pdb=" C ASN A 381 " pdb=" CB ASN A 381 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ASN A 218 " pdb=" N ASN A 218 " pdb=" C ASN A 218 " pdb=" CB ASN A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2454 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 231 " -0.063 2.00e-02 2.50e+03 3.49e-02 3.04e+01 pdb=" CG TRP A 231 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP A 231 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 231 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP A 231 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP A 231 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 231 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 231 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 231 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 231 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 70 " -0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C ALA B 70 " 0.081 2.00e-02 2.50e+03 pdb=" O ALA B 70 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 71 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 150 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C GLY C 150 " 0.081 2.00e-02 2.50e+03 pdb=" O GLY C 150 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA C 151 " -0.027 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2460 2.81 - 3.34: 14684 3.34 - 3.86: 21353 3.86 - 4.38: 26078 4.38 - 4.90: 43505 Nonbonded interactions: 108080 Sorted by model distance: nonbonded pdb=" OD1 ASP C 547 " pdb=" N ILE C 548 " model vdw 2.293 3.120 nonbonded pdb=" O ASP A 232 " pdb=" OD1 ASP A 232 " model vdw 2.385 3.040 nonbonded pdb=" OD1 ASP C 168 " pdb=" N GLU C 169 " model vdw 2.398 3.120 nonbonded pdb=" O THR B 594 " pdb=" OG1 THR B 594 " model vdw 2.420 3.040 nonbonded pdb=" O ASP A 176 " pdb=" OD1 ASP A 176 " model vdw 2.443 3.040 ... (remaining 108075 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 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 through 78 or (resid 79 and (nam \ e N or name CA or name C or name O or name CB )) or resid 80 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 182 or (resid 183 through 185 and (name N or n \ ame CA or name C or name O or name CB )) or resid 186 through 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 22 \ 7 or resid 229 through 237 or (resid 238 through 241 and (name N or name CA or n \ ame C or name O or name CB )) or resid 242 or (resid 243 through 245 and (name N \ or name CA or name C or name O or name CB )) or resid 246 through 250 or (resid \ 251 through 253 and (name N or name CA or name C or name O or name CB )) or res \ id 254 through 255 or (resid 256 through 257 and (name N or name CA or name C or \ name O or name CB )) or resid 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 261 or (resid 262 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 264 through 268 o \ r (resid 269 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 70 or (resid 271 through 272 and (name N or name CA or name C or name O or name \ CB )) or resid 273 or (resid 274 and (name N or name CA or name C or name O or n \ ame CB )) or resid 275 or (resid 276 and (name N or name CA or name C or name O \ or name CB )) or resid 277 or (resid 278 through 279 and (name N or name CA or n \ ame C or name O or name CB )) or resid 280 or (resid 281 through 293 and (name N \ or name CA or name C or name O or name CB )) or resid 294 or (resid 295 and (na \ me N or name CA or name C or name O or name CB )) or resid 296 through 312 or (r \ esid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 t \ hrough 391 or (resid 392 and (name N or name CA or name C or name O or name CB ) \ ) or resid 393 through 397 or (resid 398 and (name N or name CA or name C or nam \ e O or name CB )) or resid 399 through 470 or (resid 471 and (name N or name CA \ or name C or name O or name CB )) or resid 472 or (resid 473 through 474 and (na \ me N or name CA or name C or name O or name CB )) or resid 475 through 511 or (r \ esid 512 and (name N or name CA or name C or name O or name CB )) or resid 513 t \ hrough 547 or (resid 548 and (name N or name CA or name C or name O or name CB ) \ ) or resid 549 or (resid 550 through 552 and (name N or name CA or name C or nam \ e O or name CB )) or resid 553 through 557 or (resid 558 through 561 and (name N \ or name CA or name C or name O or name CB )) or resid 562 through 573 or (resid \ 574 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 or (resid 585 through 592 and (name N or name CA or name C or name O or n \ ame CB )) or resid 593 through 594 or (resid 595 through 599 and (name N or name \ CA or name C or name O or name CB )) or resid 600 or (resid 601 and (name N or \ name CA or name C or name O or name CB )) or (resid 602 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 (n \ ame N or name CA or name C or name O or name CB )) or (resid 636 through 668 and \ (name N or name CA or name C or name O or name CB )) or resid 669 through 673 o \ r (resid 674 through 682 and (name N or name CA or name C or name O or name CB ) \ ) or resid 683 through 695)) selection = (chain 'B' and (resid 1 through 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 through 197 or (resid 198 and (n \ ame N or name CA or name C or name O or name CB )) or resid 199 through 227 or r \ esid 229 through 237 or (resid 238 through 241 and (name N or name CA or name C \ or name O or name CB )) or resid 242 through 271 or (resid 272 and (name N or na \ me CA or name C or name O or name CB )) or resid 273 through 277 or (resid 278 t \ hrough 279 and (name N or name CA or name C or name O or name CB )) or resid 280 \ through 281 or (resid 282 through 293 and (name N or name CA or name C or name \ O or name CB )) or resid 294 through 391 or (resid 392 and (name N or name CA or \ name C or name O or name CB )) or resid 393 through 470 or (resid 471 and (name \ N or name CA or name C or name O or name CB )) or resid 472 or (resid 473 throu \ gh 474 and (name N or name CA or name C or name O or name CB )) or resid 475 thr \ ough 511 or (resid 512 and (name N or name CA or name C or name O or name CB )) \ or resid 513 through 550 or (resid 551 through 552 and (name N or name CA or nam \ e C or name O or name CB )) or resid 553 through 567 or (resid 568 through 569 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 570 through 58 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 584 through \ 592 and (name N or name CA or name C or name O or name CB )) or resid 593 throu \ gh 695)) selection = (chain 'C' and (resid 1 through 78 or (resid 79 and (name N or name CA or name C \ or name O or name CB )) or resid 80 through 85 or (resid 86 and (name N or name \ CA or name C or name O or name CB )) or resid 87 through 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 168 or \ (resid 169 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 0 through 182 or (resid 183 through 185 and (name N or name CA or name C or name \ O or name CB )) or resid 186 through 227 or resid 229 through 242 or (resid 243 \ through 245 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 46 through 250 or (resid 251 through 253 and (name N or name CA or name C or nam \ e O or name CB )) or resid 254 through 255 or (resid 256 through 257 and (name N \ or name CA or name C or name O or name CB )) or resid 258 or (resid 259 and (na \ me N or name CA or name C or name O or name CB )) or resid 260 through 261 or (r \ esid 262 through 263 and (name N or name CA or name C or name O or name CB )) or \ resid 264 through 290 or (resid 291 through 293 and (name N or name CA or name \ C or name O or name CB )) or resid 294 or (resid 295 and (name N or name CA or n \ ame C or name O or name CB )) or resid 296 through 397 or (resid 398 and (name N \ or name CA or name C or name O or name CB )) or resid 399 through 557 or (resid \ 558 through 561 and (name N or name CA or name C or name O or name CB )) or res \ id 562 through 567 or (resid 568 through 569 and (name N or name CA or name C or \ name O or name CB )) or (resid 570 through 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 or (resid 585 through 592 and (name N or n \ ame CA or name C or name O or name CB )) or resid 593 through 594 or (resid 595 \ through 599 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 0 or (resid 601 and (name N or name CA or name C or name O or name CB )) or (res \ id 602 through 621 and (name N or name CA or name C or name O or name CB )) or r \ esid 622 through 673 or (resid 674 through 682 and (name N or name CA or name C \ or name O or name CB )) or resid 683 through 695)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.190 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.014 0.186 14931 Z= 1.087 Angle : 1.758 14.849 20361 Z= 1.304 Chirality : 0.110 0.750 2457 Planarity : 0.009 0.047 2691 Dihedral : 14.216 88.934 5224 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.65 % Allowed : 7.14 % Favored : 91.20 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2080 helix: 0.27 (0.20), residues: 640 sheet: 0.46 (0.24), residues: 435 loop : -1.13 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG C 426 TYR 0.056 0.006 TYR B 156 PHE 0.038 0.006 PHE B 376 TRP 0.079 0.009 TRP A 231 HIS 0.025 0.005 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.01419 / 1.09 (14931) covalent geometry : angle 1.75834 / 1.30 (20361) hydrogen bonds : bond 0.20932 / 14.19 ( 759) hydrogen bonds : angle 7.46304 / 5.29 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.8499 (tmm) cc_final: 0.8205 (tmm) REVERT: A 297 LEU cc_start: 0.9591 (mt) cc_final: 0.9346 (tt) REVERT: A 392 MET cc_start: 0.8954 (ptm) cc_final: 0.8475 (ppp) REVERT: A 440 MET cc_start: 0.7996 (mmp) cc_final: 0.7107 (mmp) REVERT: A 490 ASP cc_start: 0.7641 (p0) cc_final: 0.7437 (m-30) REVERT: A 519 MET cc_start: 0.8486 (mmt) cc_final: 0.7930 (mtm) REVERT: C 94 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 188 MET cc_start: 0.8732 (ppp) cc_final: 0.7925 (ppp) REVERT: C 190 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6983 (mt-10) REVERT: C 541 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8254 (tp) outliers start: 21 outliers final: 4 residues processed: 123 average time/residue: 0.1072 time to fit residues: 20.6384 Evaluate side-chains 83 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 541 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN A 26 GLN A 47 GLN A 146 ASN A 167 GLN A 218 ASN A 474 ASN A 525 GLN A 539 GLN B 200 GLN B 209 HIS B 291 ASN B 381 ASN B 525 GLN B 532 HIS C 47 GLN C 363 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.098204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064691 restraints weight = 44504.062| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.14 r_work: 0.2996 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14931 Z= 0.170 Angle : 0.645 8.540 20361 Z= 0.348 Chirality : 0.049 0.388 2457 Planarity : 0.004 0.041 2691 Dihedral : 7.224 122.828 2311 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 9.92 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2080 helix: 1.68 (0.21), residues: 633 sheet: 0.63 (0.24), residues: 460 loop : -0.86 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 319 TYR 0.016 0.002 TYR A 380 PHE 0.013 0.002 PHE C 145 TRP 0.034 0.004 TRP A 231 HIS 0.008 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (14931) covalent geometry : angle 0.64459 / 0.35 (20361) hydrogen bonds : bond 0.05785 / 3.88 ( 759) hydrogen bonds : angle 5.07637 / 3.60 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.585 Fit side-chains REVERT: A 392 MET cc_start: 0.9136 (ptm) cc_final: 0.8726 (ppp) REVERT: A 490 ASP cc_start: 0.7196 (p0) cc_final: 0.6987 (m-30) REVERT: A 519 MET cc_start: 0.8308 (mmt) cc_final: 0.7857 (mtm) REVERT: B 323 MET cc_start: 0.8569 (mtt) cc_final: 0.8320 (mtt) REVERT: B 369 MET cc_start: 0.9144 (mmm) cc_final: 0.8906 (mmm) REVERT: B 392 MET cc_start: 0.7740 (tpp) cc_final: 0.7351 (tpp) REVERT: C 188 MET cc_start: 0.8875 (ppp) cc_final: 0.8617 (ppp) outliers start: 19 outliers final: 6 residues processed: 94 average time/residue: 0.0906 time to fit residues: 14.5842 Evaluate side-chains 78 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 425 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 36 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 61 optimal weight: 50.0000 chunk 52 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.098111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063164 restraints weight = 73107.558| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 5.18 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14931 Z= 0.137 Angle : 0.552 8.767 20361 Z= 0.294 Chirality : 0.046 0.357 2457 Planarity : 0.003 0.045 2691 Dihedral : 6.584 136.146 2307 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.58 % Allowed : 10.98 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2080 helix: 2.10 (0.21), residues: 632 sheet: 0.92 (0.24), residues: 472 loop : -0.77 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 230 TYR 0.012 0.001 TYR B 68 PHE 0.012 0.001 PHE C 145 TRP 0.024 0.002 TRP A 231 HIS 0.006 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14931) covalent geometry : angle 0.55237 / 0.29 (20361) hydrogen bonds : bond 0.04653 / 3.09 ( 759) hydrogen bonds : angle 4.52862 / 3.23 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.466 Fit side-chains REVERT: A 392 MET cc_start: 0.8798 (ptm) cc_final: 0.8331 (ppp) REVERT: A 466 MET cc_start: 0.7893 (mmm) cc_final: 0.7462 (mtp) REVERT: A 519 MET cc_start: 0.8227 (mmt) cc_final: 0.7750 (mtm) REVERT: B 201 MET cc_start: 0.8158 (mmm) cc_final: 0.7784 (mmt) REVERT: B 323 MET cc_start: 0.8412 (mtt) cc_final: 0.8154 (mtt) REVERT: C 32 MET cc_start: 0.9004 (ttp) cc_final: 0.8801 (ttt) REVERT: C 188 MET cc_start: 0.8737 (ppp) cc_final: 0.8501 (tmm) REVERT: C 369 MET cc_start: 0.8735 (mmm) cc_final: 0.8219 (mmt) REVERT: C 491 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7183 (ttt) outliers start: 20 outliers final: 9 residues processed: 89 average time/residue: 0.0856 time to fit residues: 13.3207 Evaluate side-chains 80 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 117 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060068 restraints weight = 50526.615| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.32 r_work: 0.2887 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14931 Z= 0.271 Angle : 0.647 10.703 20361 Z= 0.342 Chirality : 0.048 0.282 2457 Planarity : 0.004 0.055 2691 Dihedral : 6.683 151.993 2306 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.71 % Allowed : 10.60 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2080 helix: 1.89 (0.21), residues: 635 sheet: 0.72 (0.25), residues: 464 loop : -0.83 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 426 TYR 0.021 0.002 TYR A 380 PHE 0.016 0.002 PHE C 145 TRP 0.040 0.005 TRP A 231 HIS 0.006 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.27 (14931) covalent geometry : angle 0.64696 / 0.34 (20361) hydrogen bonds : bond 0.05398 / 3.56 ( 759) hydrogen bonds : angle 4.66675 / 3.33 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.597 Fit side-chains REVERT: A 22 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7977 (ttp) REVERT: A 323 MET cc_start: 0.8675 (mtp) cc_final: 0.8392 (mtp) REVERT: A 392 MET cc_start: 0.9188 (ptm) cc_final: 0.8584 (ppp) REVERT: A 466 MET cc_start: 0.8514 (mmm) cc_final: 0.8263 (mtp) REVERT: A 519 MET cc_start: 0.8440 (mmt) cc_final: 0.7961 (mtm) REVERT: B 67 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8779 (t) REVERT: B 190 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: B 201 MET cc_start: 0.8293 (mmm) cc_final: 0.7829 (mmt) REVERT: B 323 MET cc_start: 0.8790 (mtt) cc_final: 0.8446 (mtt) REVERT: C 22 MET cc_start: 0.8286 (ttt) cc_final: 0.7918 (ttt) REVERT: C 190 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 328 ASP cc_start: 0.8600 (t0) cc_final: 0.8321 (t0) REVERT: C 369 MET cc_start: 0.8529 (mmm) cc_final: 0.7834 (mmt) outliers start: 35 outliers final: 17 residues processed: 103 average time/residue: 0.0911 time to fit residues: 16.2055 Evaluate side-chains 91 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 128 optimal weight: 50.0000 chunk 65 optimal weight: 0.0270 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.096994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063336 restraints weight = 44177.791| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.03 r_work: 0.2966 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14931 Z= 0.123 Angle : 0.515 11.681 20361 Z= 0.270 Chirality : 0.044 0.278 2457 Planarity : 0.003 0.052 2691 Dihedral : 6.349 151.503 2306 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.18 % Allowed : 12.18 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 2080 helix: 2.27 (0.21), residues: 630 sheet: 0.90 (0.25), residues: 466 loop : -0.74 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.013 0.001 TYR B 68 PHE 0.011 0.001 PHE B 207 TRP 0.024 0.002 TRP A 231 HIS 0.005 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14931) covalent geometry : angle 0.51536 / 0.27 (20361) hydrogen bonds : bond 0.04090 / 2.71 ( 759) hydrogen bonds : angle 4.27451 / 3.05 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 418 MET cc_start: 0.8242 (tpt) cc_final: 0.7956 (tpt) REVERT: A 519 MET cc_start: 0.8259 (mmt) cc_final: 0.7805 (mtm) REVERT: B 125 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8768 (t0) REVERT: B 201 MET cc_start: 0.8263 (mmm) cc_final: 0.7754 (mmt) REVERT: B 323 MET cc_start: 0.8705 (mtt) cc_final: 0.8386 (mtt) REVERT: C 190 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7652 (tm-30) REVERT: C 201 MET cc_start: 0.7815 (mmm) cc_final: 0.7580 (mmt) REVERT: C 328 ASP cc_start: 0.8509 (t0) cc_final: 0.8239 (t0) REVERT: C 369 MET cc_start: 0.8478 (mmm) cc_final: 0.8021 (mmt) REVERT: C 491 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7687 (ttt) outliers start: 28 outliers final: 15 residues processed: 97 average time/residue: 0.0953 time to fit residues: 15.7713 Evaluate side-chains 90 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 200 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 164 ASN C 123 GLN C 532 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.097937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064443 restraints weight = 44811.034| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.04 r_work: 0.2995 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14931 Z= 0.104 Angle : 0.492 11.285 20361 Z= 0.256 Chirality : 0.044 0.274 2457 Planarity : 0.003 0.052 2691 Dihedral : 6.067 149.065 2306 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.88 % Allowed : 12.26 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2080 helix: 2.41 (0.21), residues: 637 sheet: 1.08 (0.25), residues: 466 loop : -0.68 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.011 0.001 TYR B 68 PHE 0.016 0.001 PHE C 41 TRP 0.017 0.002 TRP A 231 HIS 0.003 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14931) covalent geometry : angle 0.49200 / 0.26 (20361) hydrogen bonds : bond 0.03576 / 2.36 ( 759) hydrogen bonds : angle 4.04193 / 2.89 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 392 MET cc_start: 0.9131 (ppp) cc_final: 0.8702 (ppp) REVERT: A 418 MET cc_start: 0.8221 (tpt) cc_final: 0.7936 (tpt) REVERT: A 519 MET cc_start: 0.8249 (mmt) cc_final: 0.7717 (mtm) REVERT: B 201 MET cc_start: 0.8304 (mmm) cc_final: 0.7817 (mmt) REVERT: B 323 MET cc_start: 0.8639 (mtt) cc_final: 0.8236 (mtt) REVERT: C 32 MET cc_start: 0.9019 (ttp) cc_final: 0.8808 (ttt) REVERT: C 190 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7499 (mt-10) REVERT: C 201 MET cc_start: 0.7769 (mmm) cc_final: 0.7544 (mmt) REVERT: C 369 MET cc_start: 0.8570 (mmm) cc_final: 0.8200 (mmt) REVERT: C 440 MET cc_start: 0.8457 (mmp) cc_final: 0.8002 (mmp) REVERT: C 491 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7577 (ttt) outliers start: 24 outliers final: 12 residues processed: 97 average time/residue: 0.0914 time to fit residues: 15.2369 Evaluate side-chains 85 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 491 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 525 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.092839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.058776 restraints weight = 45285.481| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.07 r_work: 0.2866 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.061 14931 Z= 0.399 Angle : 0.737 10.665 20361 Z= 0.387 Chirality : 0.051 0.267 2457 Planarity : 0.005 0.058 2691 Dihedral : 6.429 146.390 2306 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.80 % Allowed : 12.26 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 2080 helix: 1.97 (0.21), residues: 638 sheet: 0.58 (0.24), residues: 468 loop : -0.81 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 409 TYR 0.030 0.002 TYR A 380 PHE 0.019 0.003 PHE A 493 TRP 0.047 0.005 TRP A 231 HIS 0.009 0.002 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00952 / 0.40 (14931) covalent geometry : angle 0.73715 / 0.39 (20361) hydrogen bonds : bond 0.05686 / 3.74 ( 759) hydrogen bonds : angle 4.62971 / 3.30 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.530 Fit side-chains REVERT: A 418 MET cc_start: 0.8157 (tpt) cc_final: 0.7827 (tpt) REVERT: A 519 MET cc_start: 0.8517 (mmt) cc_final: 0.8014 (mtm) REVERT: B 201 MET cc_start: 0.8341 (mmm) cc_final: 0.7785 (mmt) REVERT: B 323 MET cc_start: 0.8644 (mtt) cc_final: 0.8224 (mtt) REVERT: C 190 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7657 (tm-30) REVERT: C 201 MET cc_start: 0.8027 (mmm) cc_final: 0.7825 (mmt) REVERT: C 231 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.5944 (p-90) REVERT: C 438 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7157 (t) outliers start: 23 outliers final: 15 residues processed: 91 average time/residue: 0.0928 time to fit residues: 14.5057 Evaluate side-chains 87 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 231 TRP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 525 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 167 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 205 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.061317 restraints weight = 57403.759| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.62 r_work: 0.2903 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14931 Z= 0.130 Angle : 0.521 10.511 20361 Z= 0.273 Chirality : 0.044 0.263 2457 Planarity : 0.003 0.055 2691 Dihedral : 6.162 143.797 2306 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.50 % Allowed : 12.63 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2080 helix: 2.34 (0.21), residues: 639 sheet: 0.78 (0.25), residues: 468 loop : -0.78 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.013 0.001 TYR B 68 PHE 0.017 0.001 PHE C 41 TRP 0.026 0.003 TRP A 231 HIS 0.003 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14931) covalent geometry : angle 0.52118 / 0.27 (20361) hydrogen bonds : bond 0.04159 / 2.75 ( 759) hydrogen bonds : angle 4.20462 / 2.99 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.573 Fit side-chains REVERT: A 418 MET cc_start: 0.8273 (tpt) cc_final: 0.8030 (tpt) REVERT: A 519 MET cc_start: 0.8306 (mmt) cc_final: 0.7845 (mtm) REVERT: B 201 MET cc_start: 0.8326 (mmm) cc_final: 0.7750 (mmt) REVERT: B 323 MET cc_start: 0.8596 (mtt) cc_final: 0.8236 (mtt) REVERT: C 32 MET cc_start: 0.9093 (ttm) cc_final: 0.8852 (ttt) REVERT: C 201 MET cc_start: 0.7932 (mmm) cc_final: 0.7708 (mmt) REVERT: C 491 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7736 (ttt) outliers start: 19 outliers final: 15 residues processed: 89 average time/residue: 0.0940 time to fit residues: 14.2601 Evaluate side-chains 87 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 204 optimal weight: 0.0270 chunk 153 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 199 optimal weight: 50.0000 chunk 45 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.096310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062694 restraints weight = 44021.148| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.01 r_work: 0.2956 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14931 Z= 0.125 Angle : 0.507 10.352 20361 Z= 0.264 Chirality : 0.044 0.264 2457 Planarity : 0.003 0.053 2691 Dihedral : 5.998 141.283 2306 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.35 % Allowed : 12.93 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 2080 helix: 2.42 (0.21), residues: 645 sheet: 0.93 (0.25), residues: 452 loop : -0.74 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.011 0.001 TYR B 68 PHE 0.015 0.001 PHE C 41 TRP 0.021 0.002 TRP A 231 HIS 0.002 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14931) covalent geometry : angle 0.50739 / 0.26 (20361) hydrogen bonds : bond 0.03892 / 2.57 ( 759) hydrogen bonds : angle 4.02655 / 2.87 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.612 Fit side-chains REVERT: A 418 MET cc_start: 0.8360 (tpt) cc_final: 0.8159 (tpt) REVERT: A 519 MET cc_start: 0.8239 (mmt) cc_final: 0.7702 (mtm) REVERT: B 201 MET cc_start: 0.8474 (mmm) cc_final: 0.7934 (mmt) REVERT: B 323 MET cc_start: 0.8627 (mtt) cc_final: 0.8257 (mtt) REVERT: C 32 MET cc_start: 0.9052 (ttm) cc_final: 0.8816 (ttt) REVERT: C 201 MET cc_start: 0.7979 (mmm) cc_final: 0.7760 (mmt) REVERT: C 369 MET cc_start: 0.8580 (mmm) cc_final: 0.8144 (mmt) REVERT: C 438 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7165 (t) REVERT: C 491 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7635 (ttt) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 0.0939 time to fit residues: 14.0954 Evaluate side-chains 84 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 84 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 134 optimal weight: 0.0050 chunk 64 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 145 optimal weight: 0.0060 chunk 92 optimal weight: 6.9990 chunk 136 optimal weight: 50.0000 chunk 100 optimal weight: 7.9990 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.098568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064252 restraints weight = 60917.443| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.71 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14931 Z= 0.088 Angle : 0.479 10.334 20361 Z= 0.248 Chirality : 0.044 0.263 2457 Planarity : 0.003 0.049 2691 Dihedral : 5.742 140.472 2306 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.98 % Allowed : 13.46 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 2080 helix: 2.67 (0.21), residues: 639 sheet: 1.19 (0.26), residues: 450 loop : -0.68 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.010 0.001 TYR B 68 PHE 0.014 0.001 PHE C 41 TRP 0.012 0.001 TRP B 231 HIS 0.002 0.000 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.09 (14931) covalent geometry : angle 0.47870 / 0.25 (20361) hydrogen bonds : bond 0.03074 / 2.05 ( 759) hydrogen bonds : angle 3.80467 / 2.71 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.651 Fit side-chains REVERT: A 353 THR cc_start: 0.9390 (m) cc_final: 0.8905 (p) REVERT: A 369 MET cc_start: 0.8974 (mmt) cc_final: 0.8672 (mmm) REVERT: A 519 MET cc_start: 0.8009 (mmt) cc_final: 0.7413 (mtm) REVERT: B 201 MET cc_start: 0.8174 (mmm) cc_final: 0.7701 (mmt) REVERT: B 323 MET cc_start: 0.8231 (mtt) cc_final: 0.7920 (mtt) REVERT: C 201 MET cc_start: 0.7756 (mmm) cc_final: 0.7556 (mmt) REVERT: C 440 MET cc_start: 0.7781 (mmp) cc_final: 0.7427 (mmp) REVERT: C 491 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6974 (ttt) outliers start: 12 outliers final: 11 residues processed: 87 average time/residue: 0.0836 time to fit residues: 12.8565 Evaluate side-chains 85 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.096381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061945 restraints weight = 56364.492| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.56 r_work: 0.2929 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14931 Z= 0.149 Angle : 0.503 10.128 20361 Z= 0.261 Chirality : 0.044 0.263 2457 Planarity : 0.003 0.047 2691 Dihedral : 5.744 140.512 2306 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.28 % Allowed : 13.31 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 2080 helix: 2.61 (0.21), residues: 645 sheet: 1.19 (0.26), residues: 452 loop : -0.64 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 426 TYR 0.012 0.001 TYR A 380 PHE 0.017 0.001 PHE C 41 TRP 0.023 0.002 TRP A 231 HIS 0.003 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (14931) covalent geometry : angle 0.50283 / 0.26 (20361) hydrogen bonds : bond 0.03689 / 2.43 ( 759) hydrogen bonds : angle 3.85438 / 2.76 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3647.37 seconds wall clock time: 63 minutes 4.98 seconds (3784.98 seconds total)