Starting phenix.real_space_refine on Fri Feb 16 07:32:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogk_12882/02_2024/7ogk_12882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogk_12882/02_2024/7ogk_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogk_12882/02_2024/7ogk_12882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogk_12882/02_2024/7ogk_12882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogk_12882/02_2024/7ogk_12882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogk_12882/02_2024/7ogk_12882.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 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 Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 9} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 9} 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: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 31, 'ARG:plan': 14} 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: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 264 Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 122 Classifications: {'RNA': 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: 72 Planarities with less than four sites: {' A%rna3p_pur:plan2': 1, ' A%rna2p_pur:plan2': 5, ' A%rna2p_pur:plan': 5, ' A%rna3p_pur:plan': 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: 10.64, per 1000 atoms: 0.72 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 1.76 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: 5.22 Time building geometry restraints manager: 5.91 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: 98.64 - 105.87: 459 105.87 - 113.10: 7658 113.10 - 120.33: 7022 120.33 - 127.56: 5151 127.56 - 134.79: 71 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 - 21.37: 8560 21.37 - 42.73: 356 42.73 - 64.09: 78 64.09 - 85.46: 27 85.46 - 106.82: 3 Dihedral angle restraints: 9024 sinusoidal: 3107 harmonic: 5917 Sorted by residual: dihedral pdb=" CA GLU C 588 " pdb=" C GLU C 588 " pdb=" N ILE C 589 " pdb=" CA ILE C 589 " ideal model delta harmonic sigma weight residual 180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LYS B 661 " pdb=" C LYS B 661 " pdb=" N VAL B 662 " pdb=" CA VAL B 662 " ideal model delta harmonic sigma weight residual -180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA LYS C 675 " pdb=" C LYS C 675 " pdb=" N VAL C 676 " pdb=" CA VAL C 676 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 9021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1534 0.103 - 0.205: 803 0.205 - 0.308: 117 0.308 - 0.410: 2 0.410 - 0.513: 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 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.57e+00 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 2.520 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 2.520 nonbonded pdb=" O THR B 594 " pdb=" OG1 THR B 594 " model vdw 2.420 2.440 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 3.580 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.390 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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= 0.964 Angle : 1.755 14.849 20361 Z= 1.303 Chirality : 0.108 0.513 2457 Planarity : 0.009 0.047 2691 Dihedral : 13.821 106.824 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (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 TRP 0.079 0.009 TRP A 231 HIS 0.025 0.005 HIS A 607 PHE 0.038 0.006 PHE B 376 TYR 0.056 0.006 TYR B 156 ARG 0.022 0.002 ARG C 426 *********************** 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 fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.697 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: 0.8786 (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: 0.2540 time to fit residues: 48.4954 Evaluate side-chains 83 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 174 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 542 ASN C 47 GLN C 363 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14931 Z= 0.215 Angle : 0.597 6.586 20361 Z= 0.327 Chirality : 0.046 0.153 2457 Planarity : 0.004 0.042 2691 Dihedral : 7.644 103.556 2311 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.43 % Allowed : 10.15 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2080 helix: 1.81 (0.21), residues: 626 sheet: 0.69 (0.25), residues: 459 loop : -0.84 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 231 HIS 0.008 0.001 HIS B 487 PHE 0.013 0.002 PHE C 9 TYR 0.015 0.002 TYR A 380 ARG 0.004 0.000 ARG C 230 *********************** 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 96 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.739 Fit side-chains REVERT: A 188 MET cc_start: 0.8219 (tmm) cc_final: 0.7986 (tmm) REVERT: A 392 MET cc_start: 0.8952 (ptm) cc_final: 0.8636 (ppp) REVERT: A 519 MET cc_start: 0.8326 (mmt) cc_final: 0.7885 (mtm) REVERT: B 392 MET cc_start: 0.7761 (tpp) cc_final: 0.7398 (tpp) outliers start: 18 outliers final: 6 residues processed: 95 average time/residue: 0.2213 time to fit residues: 34.8239 Evaluate side-chains 77 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 597 ILE 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 104 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 50.0000 chunk 51 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 186 optimal weight: 0.4980 chunk 64 optimal weight: 40.0000 chunk 151 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2295 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= 0.395 Angle : 0.616 7.612 20361 Z= 0.330 Chirality : 0.047 0.189 2457 Planarity : 0.004 0.049 2691 Dihedral : 7.231 102.826 2307 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.11 % Allowed : 10.53 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2080 helix: 2.01 (0.21), residues: 632 sheet: 0.71 (0.25), residues: 466 loop : -0.88 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 231 HIS 0.006 0.001 HIS B 487 PHE 0.018 0.002 PHE A 376 TYR 0.020 0.002 TYR A 380 ARG 0.004 0.001 ARG B 319 *********************** 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 100 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 1.792 Fit side-chains REVERT: A 392 MET cc_start: 0.9002 (ptm) cc_final: 0.8582 (ppp) REVERT: A 466 MET cc_start: 0.7966 (mmm) cc_final: 0.7538 (mtp) REVERT: A 519 MET cc_start: 0.8413 (mmt) cc_final: 0.8024 (mtm) REVERT: B 125 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8774 (t0) REVERT: B 201 MET cc_start: 0.8680 (mmm) cc_final: 0.8272 (mmt) REVERT: B 212 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7904 (mm-40) REVERT: B 323 MET cc_start: 0.8716 (mtt) cc_final: 0.8505 (mtt) REVERT: C 369 MET cc_start: 0.9127 (mmm) cc_final: 0.8756 (mmt) REVERT: C 491 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7455 (ttt) outliers start: 27 outliers final: 14 residues processed: 96 average time/residue: 0.2034 time to fit residues: 33.3958 Evaluate side-chains 84 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 113 VAL 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 125 ASN Chi-restraints excluded: chain B residue 175 LEU 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 352 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 491 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 0.0000 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 126 optimal weight: 40.0000 chunk 188 optimal weight: 0.9980 chunk 200 optimal weight: 50.0000 chunk 98 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2572 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= 0.200 Angle : 0.510 11.932 20361 Z= 0.271 Chirality : 0.044 0.170 2457 Planarity : 0.003 0.051 2691 Dihedral : 6.961 102.584 2307 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.88 % Allowed : 10.98 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2080 helix: 2.31 (0.21), residues: 627 sheet: 0.92 (0.25), residues: 464 loop : -0.82 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 231 HIS 0.005 0.001 HIS B 487 PHE 0.011 0.001 PHE B 207 TYR 0.013 0.001 TYR B 68 ARG 0.003 0.000 ARG A 319 *********************** 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 97 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 1.808 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.8633 (mtp) cc_final: 0.8344 (mtm) REVERT: A 392 MET cc_start: 0.8982 (ptm) cc_final: 0.8563 (ppp) REVERT: A 519 MET cc_start: 0.8329 (mmt) cc_final: 0.7906 (mtm) REVERT: B 201 MET cc_start: 0.8626 (mmm) cc_final: 0.8093 (mmt) REVERT: B 323 MET cc_start: 0.8652 (mtt) cc_final: 0.8441 (mtt) REVERT: C 369 MET cc_start: 0.9030 (mmm) cc_final: 0.8760 (mmt) outliers start: 24 outliers final: 11 residues processed: 94 average time/residue: 0.2089 time to fit residues: 33.4483 Evaluate side-chains 82 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 B residue 451 MET 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 531 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 50.0000 chunk 113 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14931 Z= 0.343 Angle : 0.563 11.559 20361 Z= 0.296 Chirality : 0.045 0.163 2457 Planarity : 0.004 0.054 2691 Dihedral : 6.862 101.578 2306 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.41 % Allowed : 11.43 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 2080 helix: 2.32 (0.21), residues: 626 sheet: 0.84 (0.25), residues: 468 loop : -0.80 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 231 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.002 PHE B 207 TYR 0.017 0.002 TYR A 380 ARG 0.003 0.000 ARG A 325 *********************** 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 101 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 1.558 Fit side-chains REVERT: A 323 MET cc_start: 0.8682 (mtp) cc_final: 0.8377 (mtm) REVERT: A 392 MET cc_start: 0.9005 (ptm) cc_final: 0.8562 (ppp) REVERT: A 418 MET cc_start: 0.8348 (tpt) cc_final: 0.8099 (tpt) REVERT: A 519 MET cc_start: 0.8408 (mmt) cc_final: 0.7992 (mtm) REVERT: B 201 MET cc_start: 0.8676 (mmm) cc_final: 0.8150 (mmt) REVERT: C 369 MET cc_start: 0.9001 (mmm) cc_final: 0.8702 (mmt) outliers start: 31 outliers final: 16 residues processed: 95 average time/residue: 0.1930 time to fit residues: 31.3456 Evaluate side-chains 84 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 67 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 451 MET 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 352 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU 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 67 optimal weight: 50.0000 chunk 180 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 166 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2941 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= 0.202 Angle : 0.499 10.890 20361 Z= 0.263 Chirality : 0.043 0.195 2457 Planarity : 0.003 0.053 2691 Dihedral : 6.698 101.181 2306 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.80 % Allowed : 12.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2080 helix: 2.39 (0.21), residues: 628 sheet: 0.95 (0.25), residues: 467 loop : -0.76 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 231 HIS 0.003 0.001 HIS C 209 PHE 0.017 0.001 PHE C 41 TYR 0.012 0.001 TYR B 68 ARG 0.004 0.000 ARG B 153 *********************** 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 91 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 1.824 Fit side-chains REVERT: A 323 MET cc_start: 0.8643 (mtp) cc_final: 0.8359 (mtm) REVERT: A 418 MET cc_start: 0.8358 (tpt) cc_final: 0.8128 (tpt) REVERT: A 519 MET cc_start: 0.8330 (mmt) cc_final: 0.7938 (mtm) REVERT: B 201 MET cc_start: 0.8670 (mmm) cc_final: 0.8113 (mmt) outliers start: 23 outliers final: 18 residues processed: 89 average time/residue: 0.2078 time to fit residues: 31.5086 Evaluate side-chains 86 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 469 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 164 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 23 MET 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 488 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 199 optimal weight: 30.0000 chunk 124 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 532 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14931 Z= 0.136 Angle : 0.484 10.417 20361 Z= 0.253 Chirality : 0.043 0.220 2457 Planarity : 0.003 0.046 2691 Dihedral : 6.546 100.993 2306 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.95 % Allowed : 12.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2080 helix: 2.50 (0.21), residues: 636 sheet: 1.12 (0.25), residues: 462 loop : -0.71 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 231 HIS 0.002 0.001 HIS B 487 PHE 0.018 0.001 PHE C 41 TYR 0.011 0.001 TYR B 68 ARG 0.003 0.000 ARG A 308 *********************** 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 97 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 2.145 Fit side-chains REVERT: A 323 MET cc_start: 0.8641 (mtp) cc_final: 0.8318 (mtm) REVERT: A 418 MET cc_start: 0.8339 (tpt) cc_final: 0.8129 (tpt) REVERT: A 519 MET cc_start: 0.8208 (mmt) cc_final: 0.7776 (mtm) REVERT: B 164 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7999 (m110) REVERT: B 201 MET cc_start: 0.8621 (mmm) cc_final: 0.8075 (mmt) REVERT: B 451 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7634 (ptp) REVERT: B 534 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7851 (mm) REVERT: C 440 MET cc_start: 0.8304 (mmm) cc_final: 0.8042 (mmp) outliers start: 25 outliers final: 13 residues processed: 94 average time/residue: 0.2432 time to fit residues: 40.0231 Evaluate side-chains 85 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 42 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 451 MET Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 534 LEU 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 417 ASP Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 531 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 chunk 126 optimal weight: 6.9990 chunk 135 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14931 Z= 0.163 Angle : 0.477 9.973 20361 Z= 0.249 Chirality : 0.043 0.180 2457 Planarity : 0.003 0.045 2691 Dihedral : 6.421 100.415 2306 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.65 % Allowed : 12.56 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 2080 helix: 2.59 (0.21), residues: 637 sheet: 1.16 (0.25), residues: 459 loop : -0.70 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 231 HIS 0.002 0.001 HIS B 487 PHE 0.015 0.001 PHE C 41 TYR 0.011 0.001 TYR B 68 ARG 0.002 0.000 ARG C 153 *********************** 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 fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.605 Fit side-chains REVERT: A 418 MET cc_start: 0.8350 (tpt) cc_final: 0.8133 (tpt) REVERT: A 519 MET cc_start: 0.8229 (mmt) cc_final: 0.7737 (mtm) REVERT: B 201 MET cc_start: 0.8622 (mmm) cc_final: 0.8109 (mmt) REVERT: B 534 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7836 (mm) REVERT: C 492 ASP cc_start: 0.7992 (p0) cc_final: 0.7737 (p0) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.2154 time to fit residues: 32.3386 Evaluate side-chains 87 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 42 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 B residue 534 LEU 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 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL 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 181 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 chunk 57 optimal weight: 30.0000 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14931 Z= 0.233 Angle : 0.501 9.661 20361 Z= 0.260 Chirality : 0.043 0.176 2457 Planarity : 0.003 0.042 2691 Dihedral : 6.396 99.772 2306 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.73 % Allowed : 12.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2080 helix: 2.61 (0.21), residues: 637 sheet: 1.08 (0.25), residues: 460 loop : -0.71 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 231 HIS 0.003 0.001 HIS C 209 PHE 0.014 0.001 PHE C 41 TYR 0.011 0.001 TYR B 68 ARG 0.002 0.000 ARG A 325 *********************** 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 91 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 1.680 Fit side-chains REVERT: A 392 MET cc_start: 0.8996 (ppp) cc_final: 0.8629 (ppp) REVERT: A 418 MET cc_start: 0.8331 (tpt) cc_final: 0.8121 (tpt) REVERT: A 519 MET cc_start: 0.8317 (mmt) cc_final: 0.7824 (mtm) REVERT: B 201 MET cc_start: 0.8655 (mmm) cc_final: 0.8143 (mmt) REVERT: B 534 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8000 (mm) REVERT: C 492 ASP cc_start: 0.8011 (p0) cc_final: 0.7724 (p0) outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 0.2045 time to fit residues: 32.2937 Evaluate side-chains 86 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 17 THR 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 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL 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 196 optimal weight: 0.1980 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 136 optimal weight: 40.0000 chunk 206 optimal weight: 30.0000 chunk 189 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14931 Z= 0.214 Angle : 0.493 9.423 20361 Z= 0.256 Chirality : 0.043 0.179 2457 Planarity : 0.003 0.041 2691 Dihedral : 6.277 99.180 2306 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.58 % Allowed : 12.63 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.19), residues: 2080 helix: 2.66 (0.21), residues: 637 sheet: 1.07 (0.25), residues: 471 loop : -0.69 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 231 HIS 0.002 0.001 HIS A 209 PHE 0.015 0.001 PHE C 41 TYR 0.011 0.001 TYR B 68 ARG 0.002 0.000 ARG B 545 ********************** 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 89 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 1.707 Fit side-chains REVERT: A 392 MET cc_start: 0.8981 (ppp) cc_final: 0.8625 (ppp) REVERT: A 519 MET cc_start: 0.8173 (mmt) cc_final: 0.7691 (mtm) REVERT: B 201 MET cc_start: 0.8688 (mmm) cc_final: 0.8136 (mmt) REVERT: B 323 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8425 (ptp) REVERT: B 534 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (mm) REVERT: C 492 ASP cc_start: 0.7986 (p0) cc_final: 0.7729 (p0) outliers start: 20 outliers final: 18 residues processed: 88 average time/residue: 0.2093 time to fit residues: 31.6284 Evaluate side-chains 89 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 42 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 323 MET Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL 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 174 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 68 optimal weight: 40.0000 chunk 168 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 520 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.094961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060058 restraints weight = 60976.282| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.71 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 14931 Z= 0.514 Angle : 0.637 19.276 20361 Z= 0.332 Chirality : 0.046 0.281 2457 Planarity : 0.004 0.066 2691 Dihedral : 6.326 98.471 2306 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.73 % Allowed : 12.93 % Favored : 85.34 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2080 helix: 2.51 (0.21), residues: 637 sheet: 0.86 (0.25), residues: 473 loop : -0.74 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 231 HIS 0.004 0.001 HIS C 209 PHE 0.014 0.002 PHE B 207 TYR 0.019 0.002 TYR A 380 ARG 0.004 0.001 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.76 seconds wall clock time: 46 minutes 3.89 seconds (2763.89 seconds total)