Starting phenix.real_space_refine on Wed Feb 14 17:32:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2x_21533/02_2024/6w2x_21533_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2x_21533/02_2024/6w2x_21533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2x_21533/02_2024/6w2x_21533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2x_21533/02_2024/6w2x_21533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2x_21533/02_2024/6w2x_21533_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2x_21533/02_2024/6w2x_21533_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 46 5.16 5 Cl 2 4.86 5 C 6455 2.51 5 N 1620 2.21 5 O 1733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "B GLU 649": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4934 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 676, 4920 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 477 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 304 Conformer: "B" Number of residues, atoms: 676, 4920 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 477 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 304 bond proxies already assigned to first conformer: 5027 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 4724 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain breaks: 4 Unresolved non-hydrogen bonds: 599 Unresolved non-hydrogen angles: 729 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 13, 'ASP:plan': 20, 'PHE:plan': 1, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 331 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATRP A 278 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 278 " occ=0.50 residue: pdb=" N L9Q A 905 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q A 905 " occ=0.99 residue: pdb=" N L9Q B1003 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q B1003 " occ=0.99 Time building chain proxies: 8.53, per 1000 atoms: 0.87 Number of scatterers: 9860 At special positions: 0 Unit cell: (137.188, 99.6957, 174.681, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 46 16.00 P 3 15.00 Mg 1 11.99 O 1733 8.00 N 1620 7.00 C 6455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 644 " distance=1.76 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 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 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 901 " - " ASN A 397 " " NAG A 902 " - " ASN A 365 " " NAG C 1 " - " ASN A 323 " " NAG D 1 " - " ASN B 404 " Time building additional restraints: 4.14 Conformation dependent library (CDL) restraints added in 2.9 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 12 sheets defined 48.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.873A pdb=" N THR A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 4.373A pdb=" N ARG A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 removed outlier: 3.535A pdb=" N SER A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.583A pdb=" N LYS A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 4.002A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 removed outlier: 3.650A pdb=" N VAL A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 4.050A pdb=" N CYS A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 326 through 336 removed outlier: 4.071A pdb=" N VAL A 330 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 335 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 367 removed outlier: 3.614A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.667A pdb=" N SER A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 498 removed outlier: 3.837A pdb=" N SER A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.878A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Proline residue: A 529 - end of helix Processing helix chain 'A' and resid 543 through 575 removed outlier: 3.583A pdb=" N GLN A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A 568 " --> pdb=" O MET A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 614 removed outlier: 3.678A pdb=" N TYR A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 595 " --> pdb=" O TRP A 591 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 673 removed outlier: 3.768A pdb=" N LYS A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 663 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 709 removed outlier: 4.547A pdb=" N ARG A 686 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 695 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 696 " --> pdb=" O TYR A 693 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 703 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 715 through 732 removed outlier: 4.583A pdb=" N ALA A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA A 723 " --> pdb=" O PHE A 719 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 745 removed outlier: 3.731A pdb=" N THR A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 110 through 122 removed outlier: 4.153A pdb=" N ALA B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.832A pdb=" N ILE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.736A pdb=" N LYS B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 removed outlier: 4.310A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.614A pdb=" N ASN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 removed outlier: 3.821A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.651A pdb=" N ARG B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 377 removed outlier: 3.586A pdb=" N ASP B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 482 through 505 removed outlier: 3.975A pdb=" N ILE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 519 through 538 removed outlier: 3.641A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 583 removed outlier: 4.100A pdb=" N GLU B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 618 removed outlier: 3.671A pdb=" N LEU B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 598 " --> pdb=" O ASP B 594 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 608 " --> pdb=" O MET B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 677 Processing helix chain 'B' and resid 689 through 712 removed outlier: 3.628A pdb=" N PHE B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 749 removed outlier: 3.693A pdb=" N THR B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 741 " --> pdb=" O CYS B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix removed outlier: 3.909A pdb=" N LEU B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 92 through 100 removed outlier: 6.614A pdb=" N ARG A 51 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LYS A 95 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 53 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE A 97 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 55 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N HIS A 99 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA A 57 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 149 Processing sheet with id= C, first strand: chain 'A' and resid 223 through 226 removed outlier: 7.197A pdb=" N THR A 194 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N PHE A 226 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN A 196 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 248 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 272 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLY A 247 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 274 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 307 through 310 removed outlier: 3.541A pdb=" N THR A 307 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.926A pdb=" N PHE A 401 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 463 through 467 removed outlier: 6.300A pdb=" N SER A 636 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 466 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 638 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 622 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 98 through 104 Processing sheet with id= H, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= I, first strand: chain 'B' and resid 228 through 232 removed outlier: 3.539A pdb=" N THR B 200 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE B 250 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU B 201 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLN B 203 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLN B 254 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN B 278 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY B 253 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE B 280 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.116A pdb=" N GLY B 440 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 448 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 429 through 431 Processing sheet with id= L, first strand: chain 'B' and resid 622 through 627 444 hydrogen bonds defined for protein. 1251 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: 2.43 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1515 1.32 - 1.45: 2997 1.45 - 1.59: 5509 1.59 - 1.72: 4 1.72 - 1.86: 72 Bond restraints: 10097 Sorted by residual: bond pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta sigma weight residual 1.454 1.500 -0.046 1.17e-02 7.31e+03 1.52e+01 bond pdb=" CA SER A 149 " pdb=" CB SER A 149 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.55e-02 4.16e+03 1.40e+01 bond pdb=" CA SER A 152 " pdb=" CB SER A 152 " ideal model delta sigma weight residual 1.531 1.476 0.055 1.52e-02 4.33e+03 1.30e+01 bond pdb=" C11 L9Q A 905 " pdb=" O3 L9Q A 905 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 L9Q B1003 " pdb=" O3 L9Q B1003 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 10092 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.55: 272 106.55 - 113.41: 5635 113.41 - 120.27: 3558 120.27 - 127.12: 4223 127.12 - 133.98: 131 Bond angle restraints: 13819 Sorted by residual: angle pdb=" CA SER A 149 " pdb=" C SER A 149 " pdb=" O SER A 149 " ideal model delta sigma weight residual 120.80 115.94 4.86 1.11e+00 8.12e-01 1.92e+01 angle pdb=" C HIS A 643 " pdb=" CA HIS A 643 " pdb=" CB HIS A 643 " ideal model delta sigma weight residual 110.22 103.70 6.52 1.67e+00 3.59e-01 1.52e+01 angle pdb=" CA HIS B 652 " pdb=" C HIS B 652 " pdb=" O HIS B 652 " ideal model delta sigma weight residual 122.63 117.70 4.93 1.29e+00 6.01e-01 1.46e+01 angle pdb=" O3P L9Q A 905 " pdb=" P L9Q A 905 " pdb=" O4P L9Q A 905 " ideal model delta sigma weight residual 98.21 109.24 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O3P L9Q B1003 " pdb=" P L9Q B1003 " pdb=" O4P L9Q B1003 " ideal model delta sigma weight residual 98.21 109.24 -11.03 3.00e+00 1.11e-01 1.35e+01 ... (remaining 13814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5635 24.18 - 48.37: 273 48.37 - 72.55: 14 72.55 - 96.73: 2 96.73 - 120.92: 6 Dihedral angle restraints: 5930 sinusoidal: 2023 harmonic: 3907 Sorted by residual: dihedral pdb=" CB CYS B 553 " pdb=" SG CYS B 553 " pdb=" SG CYS B 648 " pdb=" CB CYS B 648 " ideal model delta sinusoidal sigma weight residual 93.00 138.87 -45.87 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS A 103 " pdb=" SG CYS A 103 " pdb=" SG CYS A 129 " pdb=" CB CYS A 129 " ideal model delta sinusoidal sigma weight residual -86.00 -128.95 42.95 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 644 " pdb=" CB CYS A 644 " ideal model delta sinusoidal sigma weight residual 93.00 135.62 -42.62 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 5927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1597 0.101 - 0.202: 56 0.202 - 0.303: 2 0.303 - 0.404: 0 0.404 - 0.505: 3 Chirality restraints: 1658 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.90 0.50 2.00e-02 2.50e+03 6.38e+02 chirality pdb=" C1 NAG D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.88 0.48 2.00e-02 2.50e+03 5.74e+02 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 397 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 1655 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 152 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C SER A 152 " 0.067 2.00e-02 2.50e+03 pdb=" O SER A 152 " -0.026 2.00e-02 2.50e+03 pdb=" N SER A 153 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 148 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C LEU A 148 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A 148 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 149 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 703 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.92e+00 pdb=" N PRO A 704 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 704 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 704 " -0.041 5.00e-02 4.00e+02 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 58 2.61 - 3.18: 8804 3.18 - 3.75: 13425 3.75 - 4.33: 17947 4.33 - 4.90: 30215 Nonbonded interactions: 70449 Sorted by model distance: nonbonded pdb=" O4 NAG D 1 " pdb=" N2 NAG D 2 " model vdw 2.034 2.520 nonbonded pdb=" OD1 ASN A 694 " pdb=" N VAL A 695 " model vdw 2.095 2.520 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.183 2.440 nonbonded pdb=" O GLY A 151 " pdb=" O10 SGG A 906 " model vdw 2.220 2.440 nonbonded pdb=" O GLU A 309 " pdb=" OG1 THR A 420 " model vdw 2.236 2.440 ... (remaining 70444 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.390 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: 11.370 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 33.910 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.005 0.072 10097 Z= 0.336 Angle : 0.752 11.033 13819 Z= 0.385 Chirality : 0.048 0.505 1658 Planarity : 0.004 0.075 1716 Dihedral : 13.836 120.917 3395 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -3.47 (0.21), residues: 1330 helix: -1.16 (0.19), residues: 662 sheet: -1.62 (0.38), residues: 205 loop : -4.30 (0.21), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 143 HIS 0.003 0.001 HIS A 685 PHE 0.013 0.001 PHE A 624 TYR 0.014 0.001 TYR B 171 ARG 0.004 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 LEU cc_start: 0.8261 (tp) cc_final: 0.7171 (mp) REVERT: B 666 LEU cc_start: 0.8603 (mt) cc_final: 0.8364 (mp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2082 time to fit residues: 42.2521 Evaluate side-chains 88 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 63 optimal weight: 0.0030 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 511 ASN B 150 ASN B 180 ASN B 278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10097 Z= 0.194 Angle : 0.578 8.647 13819 Z= 0.290 Chirality : 0.043 0.344 1658 Planarity : 0.004 0.055 1716 Dihedral : 9.159 102.563 1641 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.69 % Allowed : 10.38 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.94 (0.23), residues: 1330 helix: 0.07 (0.21), residues: 669 sheet: -1.18 (0.39), residues: 202 loop : -3.41 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 656 HIS 0.004 0.001 HIS A 176 PHE 0.017 0.001 PHE B 582 TYR 0.023 0.001 TYR B 273 ARG 0.010 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 LEU cc_start: 0.8330 (tp) cc_final: 0.7274 (mp) outliers start: 6 outliers final: 3 residues processed: 95 average time/residue: 0.1839 time to fit residues: 26.9100 Evaluate side-chains 82 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 128 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.0000 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN A 572 HIS B 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10097 Z= 0.292 Angle : 0.641 12.839 13819 Z= 0.322 Chirality : 0.046 0.275 1658 Planarity : 0.005 0.063 1716 Dihedral : 8.028 70.920 1641 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.85 % Allowed : 14.76 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.59 (0.24), residues: 1330 helix: 0.32 (0.21), residues: 668 sheet: -1.37 (0.36), residues: 226 loop : -3.03 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 290 HIS 0.009 0.001 HIS A 176 PHE 0.023 0.002 PHE B 582 TYR 0.017 0.002 TYR B 268 ARG 0.009 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.961 Fit side-chains REVERT: A 125 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 365 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8536 (mt) outliers start: 16 outliers final: 7 residues processed: 98 average time/residue: 0.1838 time to fit residues: 27.4645 Evaluate side-chains 84 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.0020 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 81 optimal weight: 0.3980 chunk 121 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10097 Z= 0.152 Angle : 0.527 8.842 13819 Z= 0.262 Chirality : 0.041 0.253 1658 Planarity : 0.004 0.057 1716 Dihedral : 7.368 70.896 1641 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.38 % Allowed : 17.65 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.05 (0.24), residues: 1330 helix: 0.69 (0.22), residues: 665 sheet: -1.06 (0.36), residues: 221 loop : -2.63 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.003 0.001 HIS A 305 PHE 0.015 0.001 PHE B 582 TYR 0.028 0.001 TYR B 273 ARG 0.010 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.028 Fit side-chains REVERT: A 125 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8445 (tp) outliers start: 12 outliers final: 5 residues processed: 95 average time/residue: 0.1670 time to fit residues: 25.2000 Evaluate side-chains 85 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 692 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10097 Z= 0.211 Angle : 0.548 8.244 13819 Z= 0.276 Chirality : 0.042 0.236 1658 Planarity : 0.004 0.057 1716 Dihedral : 7.189 67.615 1641 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.73 % Allowed : 18.80 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.24), residues: 1330 helix: 0.77 (0.22), residues: 666 sheet: -0.84 (0.36), residues: 213 loop : -2.77 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 676 HIS 0.005 0.001 HIS A 176 PHE 0.014 0.001 PHE A 249 TYR 0.024 0.001 TYR B 273 ARG 0.010 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.072 Fit side-chains REVERT: A 125 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8556 (mp) REVERT: B 365 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8569 (mt) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.1752 time to fit residues: 25.1619 Evaluate side-chains 90 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10097 Z= 0.199 Angle : 0.532 9.280 13819 Z= 0.267 Chirality : 0.042 0.222 1658 Planarity : 0.004 0.052 1716 Dihedral : 7.036 67.067 1641 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.19 % Allowed : 19.15 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.85 (0.24), residues: 1330 helix: 0.87 (0.21), residues: 665 sheet: -0.72 (0.36), residues: 213 loop : -2.71 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 283 HIS 0.003 0.001 HIS A 685 PHE 0.013 0.001 PHE A 624 TYR 0.025 0.001 TYR B 273 ARG 0.009 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.106 Fit side-chains REVERT: A 125 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8554 (mp) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 0.1745 time to fit residues: 26.9803 Evaluate side-chains 97 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10097 Z= 0.216 Angle : 0.551 8.069 13819 Z= 0.277 Chirality : 0.042 0.217 1658 Planarity : 0.004 0.055 1716 Dihedral : 7.018 71.232 1641 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.42 % Allowed : 19.15 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.24), residues: 1330 helix: 0.87 (0.22), residues: 663 sheet: -0.69 (0.36), residues: 213 loop : -2.67 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.005 0.001 HIS A 176 PHE 0.014 0.001 PHE A 624 TYR 0.027 0.001 TYR B 273 ARG 0.010 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.004 Fit side-chains REVERT: A 125 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8591 (mp) REVERT: B 365 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8590 (mt) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 0.1732 time to fit residues: 27.0826 Evaluate side-chains 98 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10097 Z= 0.198 Angle : 0.543 11.760 13819 Z= 0.269 Chirality : 0.042 0.212 1658 Planarity : 0.004 0.051 1716 Dihedral : 6.963 74.080 1641 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.19 % Allowed : 19.38 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.73 (0.24), residues: 1330 helix: 0.92 (0.22), residues: 662 sheet: -0.62 (0.37), residues: 213 loop : -2.56 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 283 HIS 0.004 0.001 HIS A 176 PHE 0.014 0.001 PHE A 624 TYR 0.024 0.001 TYR B 273 ARG 0.010 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.922 Fit side-chains REVERT: A 125 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8588 (mp) REVERT: B 259 MET cc_start: 0.6061 (mpp) cc_final: 0.5798 (tpp) outliers start: 19 outliers final: 16 residues processed: 98 average time/residue: 0.1703 time to fit residues: 25.9773 Evaluate side-chains 96 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10097 Z= 0.215 Angle : 0.558 9.285 13819 Z= 0.279 Chirality : 0.042 0.209 1658 Planarity : 0.004 0.056 1716 Dihedral : 6.961 78.492 1641 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.08 % Allowed : 20.07 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.73 (0.24), residues: 1330 helix: 0.92 (0.22), residues: 662 sheet: -0.76 (0.36), residues: 226 loop : -2.52 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.005 0.001 HIS A 176 PHE 0.016 0.001 PHE A 624 TYR 0.024 0.001 TYR B 273 ARG 0.009 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.087 Fit side-chains REVERT: A 125 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 701 ILE cc_start: 0.9124 (tt) cc_final: 0.8869 (tt) REVERT: B 365 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8603 (mt) outliers start: 18 outliers final: 15 residues processed: 97 average time/residue: 0.1684 time to fit residues: 25.5125 Evaluate side-chains 97 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 0.0000 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10097 Z= 0.169 Angle : 0.528 9.625 13819 Z= 0.261 Chirality : 0.041 0.207 1658 Planarity : 0.004 0.054 1716 Dihedral : 6.719 80.706 1641 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.08 % Allowed : 20.53 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1330 helix: 1.03 (0.22), residues: 661 sheet: -0.51 (0.37), residues: 212 loop : -2.46 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS A 305 PHE 0.012 0.001 PHE A 624 TYR 0.025 0.001 TYR B 273 ARG 0.009 0.000 ARG A 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.026 Fit side-chains REVERT: B 259 MET cc_start: 0.6117 (mpp) cc_final: 0.5897 (tpp) REVERT: B 365 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8570 (mt) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.1738 time to fit residues: 26.4211 Evaluate side-chains 98 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 702 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132284 restraints weight = 19225.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129769 restraints weight = 25840.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127634 restraints weight = 22701.256| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10097 Z= 0.267 Angle : 0.592 9.023 13819 Z= 0.298 Chirality : 0.044 0.203 1658 Planarity : 0.004 0.058 1716 Dihedral : 6.919 84.867 1641 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.31 % Allowed : 20.65 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.78 (0.24), residues: 1330 helix: 0.84 (0.21), residues: 663 sheet: -0.77 (0.36), residues: 229 loop : -2.51 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 149 HIS 0.006 0.001 HIS A 176 PHE 0.018 0.002 PHE A 624 TYR 0.024 0.001 TYR B 663 ARG 0.009 0.000 ARG A 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.63 seconds wall clock time: 36 minutes 51.53 seconds (2211.53 seconds total)