Starting phenix.real_space_refine on Sat Sep 28 14:38:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/09_2024/8ffl_29046.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/09_2024/8ffl_29046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/09_2024/8ffl_29046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/09_2024/8ffl_29046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/09_2024/8ffl_29046.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/09_2024/8ffl_29046.cif" } resolution = 3.47 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= 0.004 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 4 5.49 5 S 110 5.16 5 C 12910 2.51 5 N 3263 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19683 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4864 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 582} Chain breaks: 7 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4884 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 585} Chain breaks: 7 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 88 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4903 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 6 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4892 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 585} Chain breaks: 7 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.31, per 1000 atoms: 0.63 Number of scatterers: 19683 At special positions: 0 Unit cell: (129.47, 128.4, 110.21, 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 110 16.00 P 4 15.00 O 3396 8.00 N 3263 7.00 C 12910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.4 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4588 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 7 sheets defined 67.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.625A pdb=" N THR A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.733A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 412 removed outlier: 5.257A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 459 removed outlier: 3.794A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.667A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 493 removed outlier: 7.049A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.675A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.658A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 530 through 534' Processing helix chain 'A' and resid 535 through 560 removed outlier: 3.728A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 Processing helix chain 'A' and resid 618 through 649 removed outlier: 4.090A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.528A pdb=" N TRP A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 719 " --> pdb=" O TRP A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.559A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.576A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.638A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.588A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 320 through 327 removed outlier: 3.742A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Proline residue: B 325 - end of helix Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.091A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 466 removed outlier: 7.156A pdb=" N LEU B 461 " --> pdb=" O TRP B 457 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 470 through 493 removed outlier: 3.827A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.720A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.662A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 529 through 560 removed outlier: 5.578A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 605 Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.783A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 711 through 717 removed outlier: 3.523A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.883A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.689A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.464A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.644A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 493 removed outlier: 3.798A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.608A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.624A pdb=" N TYR C 515 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 524 Processing helix chain 'C' and resid 530 through 534 removed outlier: 3.808A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 530 through 534' Processing helix chain 'C' and resid 536 through 560 removed outlier: 4.300A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.715A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.538A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.548A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 281 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.183A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Proline residue: D 325 - end of helix Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.525A pdb=" N MET D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 377 through 414 removed outlier: 5.257A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 414 " --> pdb=" O VAL D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 459 through 466 removed outlier: 3.708A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.701A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.323A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.572A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 528 through 559 removed outlier: 3.561A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 605 Processing helix chain 'D' and resid 618 through 649 removed outlier: 3.963A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.676A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 719 " --> pdb=" O TRP D 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.897A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.115A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 692 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG B 702 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS B 690 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS B 704 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 688 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 674 through 675 Processing sheet with id=AA4, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.984A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 674 through 675 removed outlier: 3.574A pdb=" N TYR C 675 " --> pdb=" O CYS C 678 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.012A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 674 through 675 1126 hydrogen bonds defined for protein. 3228 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: 6.48 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3391 1.33 - 1.45: 5396 1.45 - 1.57: 11195 1.57 - 1.70: 8 1.70 - 1.82: 168 Bond restraints: 20158 Sorted by residual: bond pdb=" CG MET C 640 " pdb=" SD MET C 640 " ideal model delta sigma weight residual 1.803 1.765 0.038 2.50e-02 1.60e+03 2.29e+00 bond pdb=" CA CYS D 282 " pdb=" CB CYS D 282 " ideal model delta sigma weight residual 1.525 1.534 -0.009 8.30e-03 1.45e+04 1.23e+00 bond pdb=" CB ASN C 639 " pdb=" CG ASN C 639 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.00e+00 bond pdb=" CB PRO A 283 " pdb=" CG PRO A 283 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.98e-01 bond pdb=" CA ASN C 639 " pdb=" CB ASN C 639 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.59e-02 3.96e+03 7.85e-01 ... (remaining 20153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 27039 1.87 - 3.74: 245 3.74 - 5.60: 31 5.60 - 7.47: 5 7.47 - 9.34: 2 Bond angle restraints: 27322 Sorted by residual: angle pdb=" N VAL A 649 " pdb=" CA VAL A 649 " pdb=" C VAL A 649 " ideal model delta sigma weight residual 112.80 107.63 5.17 1.15e+00 7.56e-01 2.02e+01 angle pdb=" CB MET A 433 " pdb=" CG MET A 433 " pdb=" SD MET A 433 " ideal model delta sigma weight residual 112.70 122.04 -9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" N VAL A 374 " pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 112.29 109.71 2.58 9.40e-01 1.13e+00 7.52e+00 angle pdb=" CA MET B 404 " pdb=" CB MET B 404 " pdb=" CG MET B 404 " ideal model delta sigma weight residual 114.10 109.41 4.69 2.00e+00 2.50e-01 5.50e+00 angle pdb=" N CYS C 678 " pdb=" CA CYS C 678 " pdb=" C CYS C 678 " ideal model delta sigma weight residual 107.23 111.10 -3.87 1.67e+00 3.59e-01 5.38e+00 ... (remaining 27317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10725 17.99 - 35.98: 881 35.98 - 53.97: 176 53.97 - 71.97: 55 71.97 - 89.96: 13 Dihedral angle restraints: 11850 sinusoidal: 4769 harmonic: 7081 Sorted by residual: dihedral pdb=" CA PHE D 209 " pdb=" C PHE D 209 " pdb=" N GLY D 210 " pdb=" CA GLY D 210 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE B 209 " pdb=" C PHE B 209 " pdb=" N GLY B 210 " pdb=" CA GLY B 210 " ideal model delta harmonic sigma weight residual 180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA PHE C 209 " pdb=" C PHE C 209 " pdb=" N GLY C 210 " pdb=" CA GLY C 210 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 11847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2073 0.030 - 0.060: 731 0.060 - 0.089: 217 0.089 - 0.119: 71 0.119 - 0.149: 3 Chirality restraints: 3095 Sorted by residual: chirality pdb=" CA MET B 404 " pdb=" N MET B 404 " pdb=" C MET B 404 " pdb=" CB MET B 404 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CB VAL B 84 " pdb=" CA VAL B 84 " pdb=" CG1 VAL B 84 " pdb=" CG2 VAL B 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA VAL A 649 " pdb=" N VAL A 649 " pdb=" C VAL A 649 " pdb=" CB VAL A 649 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 3092 not shown) Planarity restraints: 3358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 282 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 283 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 649 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C VAL A 649 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 649 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN A 650 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 212 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 213 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.019 5.00e-02 4.00e+02 ... (remaining 3355 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1417 2.74 - 3.28: 19694 3.28 - 3.82: 32881 3.82 - 4.36: 39124 4.36 - 4.90: 68395 Nonbonded interactions: 161511 Sorted by model distance: nonbonded pdb=" OE1 GLU C 113 " pdb=" OG1 THR C 116 " model vdw 2.199 3.040 nonbonded pdb=" O PRO D 325 " pdb=" NH2 ARG D 702 " model vdw 2.271 3.120 nonbonded pdb=" OG1 THR D 604 " pdb=" OH TYR D 629 " model vdw 2.276 3.040 nonbonded pdb=" OG SER D 646 " pdb=" OE2 GLU D 647 " model vdw 2.277 3.040 nonbonded pdb=" O PRO C 325 " pdb=" NH2 ARG C 702 " model vdw 2.286 3.120 ... (remaining 161506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 89 or (resid 90 and (name N or name CA or name \ C or name O or name CB )) or resid 91 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 414 or (resid 429 and \ (name N or name CA or name C or name O or name CB )) or resid 430 through 463 o \ r (resid 464 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 65 through 494 or (resid 495 and (name N or name CA or name C or name O or name \ CB )) or resid 496 through 530 or (resid 531 and (name N or name CA or name C or \ name O or name CB )) or resid 532 through 534 or (resid 535 and (name N or name \ CA or name C or name O or name CB )) or resid 536 through 611 or (resid 612 and \ (name N or name CA or name C or name O or name CB )) or resid 616 through 646 o \ r (resid 647 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 48 through 720 or resid 801)) selection = (chain 'B' and (resid 31 through 45 or resid 75 through 143 or (resid 144 and (n \ ame N or name CA or name C or name O or name CB )) or resid 145 through 414 or ( \ resid 429 and (name N or name CA or name C or name O or name CB )) or resid 430 \ through 494 or (resid 495 and (name N or name CA or name C or name O or name CB \ )) or resid 496 through 524 or resid 529 through 530 or (resid 531 and (name N o \ r name CA or name C or name O or name CB )) or resid 532 through 534 or (resid 5 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 536 through \ 598 or (resid 599 and (name N or name CA or name C or name O or name CB )) or r \ esid 600 through 608 or (resid 609 and (name N or name CA or name C or name O or \ name CB )) or resid 610 through 716 or (resid 717 and (name N or name CA or nam \ e C or name O or name CB )) or resid 718 through 720 or resid 801)) selection = (chain 'C' and (resid 31 through 45 or resid 75 through 89 or (resid 90 and (nam \ e N or name CA or name C or name O or name CB )) or resid 91 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 261 or (resid 262 and (name N or name CA or name C or name O o \ r name CB )) or resid 263 through 414 or (resid 429 and (name N or name CA or na \ me C or name O or name CB )) or resid 430 through 463 or (resid 464 and (name N \ or name CA or name C or name O or name CB )) or resid 465 through 494 or (resid \ 495 and (name N or name CA or name C or name O or name CB )) or resid 496 throug \ h 524 or resid 529 through 598 or (resid 599 and (name N or name CA or name C or \ name O or name CB )) or resid 600 through 608 or (resid 609 and (name N or name \ CA or name C or name O or name CB )) or resid 610 through 611 or (resid 612 and \ (name N or name CA or name C or name O or name CB )) or resid 616 through 646 o \ r (resid 647 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 48 through 652 or resid 655 through 720 or resid 801)) selection = (chain 'D' and (resid 31 through 45 or resid 75 through 89 or (resid 90 and (nam \ e N or name CA or name C or name O or name CB )) or resid 91 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 463 or (resid 464 and (name N or name CA or name C or name O o \ r name CB )) or resid 465 through 524 or resid 529 through 530 or (resid 531 and \ (name N or name CA or name C or name O or name CB )) or resid 532 through 534 o \ r (resid 535 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 36 through 598 or (resid 599 and (name N or name CA or name C or name O or name \ CB )) or resid 600 through 611 or (resid 612 and (name N or name CA or name C or \ name O or name CB )) or resid 616 through 646 or (resid 647 and (name N or name \ CA or name C or name O or name CB )) or resid 648 through 716 or (resid 717 and \ (name N or name CA or name C or name O or name CB )) or resid 718 through 720 o \ r resid 801)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.330 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 45.740 Find NCS groups from input model: 1.570 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.002 0.050 20158 Z= 0.153 Angle : 0.489 9.340 27322 Z= 0.277 Chirality : 0.035 0.149 3095 Planarity : 0.003 0.053 3358 Dihedral : 14.395 89.956 7262 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.14 % Allowed : 7.09 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.72 (0.17), residues: 2364 helix: 1.79 (0.14), residues: 1442 sheet: 0.92 (0.54), residues: 116 loop : 0.08 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 657 HIS 0.008 0.001 HIS A 269 PHE 0.015 0.001 PHE C 429 TYR 0.013 0.001 TYR C 98 ARG 0.006 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 2.394 Fit side-chains REVERT: A 433 MET cc_start: 0.6934 (mmp) cc_final: 0.6481 (ptt) REVERT: B 433 MET cc_start: 0.6629 (ttm) cc_final: 0.6201 (ttp) REVERT: C 289 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8077 (mt-10) REVERT: C 645 MET cc_start: 0.7207 (mtt) cc_final: 0.6980 (mtp) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.2793 time to fit residues: 67.1697 Evaluate side-chains 140 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.0870 chunk 217 optimal weight: 10.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20158 Z= 0.314 Angle : 0.522 6.175 27322 Z= 0.270 Chirality : 0.039 0.137 3095 Planarity : 0.004 0.040 3358 Dihedral : 7.189 65.935 2743 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.14 % Allowed : 7.47 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.78 (0.18), residues: 2364 helix: 1.81 (0.14), residues: 1479 sheet: 0.86 (0.53), residues: 116 loop : 0.09 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.008 0.001 HIS A 269 PHE 0.021 0.002 PHE A 540 TYR 0.014 0.001 TYR C 515 ARG 0.005 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 2.428 Fit side-chains REVERT: C 540 PHE cc_start: 0.7801 (m-10) cc_final: 0.7561 (m-80) REVERT: C 640 MET cc_start: 0.7409 (tpp) cc_final: 0.7142 (mmt) REVERT: C 644 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8417 (tt) outliers start: 24 outliers final: 11 residues processed: 172 average time/residue: 0.3017 time to fit residues: 84.2368 Evaluate side-chains 153 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 181 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN C 127 ASN C 650 ASN D 520 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20158 Z= 0.334 Angle : 0.519 7.361 27322 Z= 0.267 Chirality : 0.039 0.171 3095 Planarity : 0.004 0.044 3358 Dihedral : 7.241 62.330 2743 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.38 % Allowed : 8.56 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.68 (0.18), residues: 2364 helix: 1.78 (0.14), residues: 1480 sheet: 0.57 (0.51), residues: 116 loop : -0.03 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 333 HIS 0.008 0.001 HIS A 269 PHE 0.026 0.002 PHE A 540 TYR 0.015 0.002 TYR B 525 ARG 0.004 0.000 ARG B 702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 2.441 Fit side-chains REVERT: A 243 ASP cc_start: 0.8399 (p0) cc_final: 0.8166 (p0) REVERT: C 182 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8165 (tt) REVERT: C 540 PHE cc_start: 0.7825 (m-10) cc_final: 0.7333 (m-80) REVERT: C 644 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8428 (tt) REVERT: D 493 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6696 (mm-30) outliers start: 29 outliers final: 14 residues processed: 171 average time/residue: 0.2768 time to fit residues: 77.5561 Evaluate side-chains 159 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN D 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20158 Z= 0.175 Angle : 0.433 6.534 27322 Z= 0.226 Chirality : 0.036 0.144 3095 Planarity : 0.003 0.044 3358 Dihedral : 6.957 59.990 2743 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.24 % Allowed : 9.56 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.93 (0.18), residues: 2364 helix: 2.04 (0.14), residues: 1475 sheet: 0.54 (0.50), residues: 114 loop : -0.03 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 PHE 0.019 0.001 PHE A 540 TYR 0.012 0.001 TYR C 98 ARG 0.003 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 2.468 Fit side-chains REVERT: B 404 MET cc_start: 0.9124 (mmt) cc_final: 0.8902 (mmt) REVERT: C 644 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8486 (tt) REVERT: D 493 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: D 521 HIS cc_start: 0.6420 (t70) cc_final: 0.6195 (t70) outliers start: 26 outliers final: 13 residues processed: 170 average time/residue: 0.2799 time to fit residues: 77.6632 Evaluate side-chains 155 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 ASN D 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20158 Z= 0.217 Angle : 0.449 7.445 27322 Z= 0.233 Chirality : 0.036 0.155 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.804 62.489 2743 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 9.90 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.95 (0.18), residues: 2364 helix: 2.05 (0.14), residues: 1474 sheet: 0.43 (0.50), residues: 114 loop : 0.00 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 PHE 0.019 0.001 PHE A 540 TYR 0.010 0.001 TYR A 544 ARG 0.003 0.000 ARG B 702 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 2.144 Fit side-chains REVERT: B 128 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8430 (mp) REVERT: C 182 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8273 (tt) REVERT: C 644 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8498 (tt) REVERT: D 493 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6672 (mm-30) REVERT: D 521 HIS cc_start: 0.6476 (t70) cc_final: 0.6261 (t70) outliers start: 34 outliers final: 18 residues processed: 175 average time/residue: 0.2885 time to fit residues: 82.0980 Evaluate side-chains 163 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 0.0370 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20158 Z= 0.237 Angle : 0.457 7.952 27322 Z= 0.236 Chirality : 0.037 0.156 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.710 66.613 2743 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.43 % Allowed : 10.32 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.93 (0.18), residues: 2364 helix: 2.03 (0.14), residues: 1479 sheet: 0.42 (0.50), residues: 114 loop : -0.00 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 PHE 0.019 0.001 PHE A 540 TYR 0.013 0.001 TYR C 98 ARG 0.003 0.000 ARG B 702 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 2.447 Fit side-chains REVERT: B 128 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 404 MET cc_start: 0.9277 (mmt) cc_final: 0.8838 (mmt) REVERT: C 173 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7733 (tm-30) REVERT: C 644 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8529 (tt) REVERT: D 493 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: D 521 HIS cc_start: 0.6516 (t70) cc_final: 0.6314 (t70) outliers start: 30 outliers final: 24 residues processed: 170 average time/residue: 0.2759 time to fit residues: 76.8164 Evaluate side-chains 169 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 231 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20158 Z= 0.135 Angle : 0.412 8.736 27322 Z= 0.214 Chirality : 0.035 0.146 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.335 67.677 2743 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.33 % Allowed : 10.56 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.11 (0.18), residues: 2364 helix: 2.16 (0.14), residues: 1490 sheet: 0.50 (0.51), residues: 114 loop : 0.06 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 PHE 0.013 0.001 PHE A 540 TYR 0.013 0.001 TYR C 98 ARG 0.002 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 2.453 Fit side-chains REVERT: B 404 MET cc_start: 0.9251 (mmt) cc_final: 0.8852 (mmt) REVERT: C 644 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8480 (tt) REVERT: D 493 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6614 (mm-30) outliers start: 28 outliers final: 17 residues processed: 177 average time/residue: 0.2932 time to fit residues: 83.4632 Evaluate side-chains 163 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20158 Z= 0.203 Angle : 0.448 9.042 27322 Z= 0.229 Chirality : 0.036 0.183 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.271 66.473 2743 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.00 % Allowed : 11.04 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.14 (0.18), residues: 2364 helix: 2.19 (0.14), residues: 1477 sheet: 0.49 (0.50), residues: 114 loop : 0.10 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 PHE 0.016 0.001 PHE A 540 TYR 0.011 0.001 TYR C 98 ARG 0.003 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 2.181 Fit side-chains REVERT: B 102 ASN cc_start: 0.6684 (m-40) cc_final: 0.6352 (m110) REVERT: C 644 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8546 (tt) REVERT: D 493 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6636 (mm-30) outliers start: 21 outliers final: 17 residues processed: 166 average time/residue: 0.2842 time to fit residues: 76.5579 Evaluate side-chains 164 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20158 Z= 0.149 Angle : 0.419 9.246 27322 Z= 0.216 Chirality : 0.035 0.182 3095 Planarity : 0.003 0.046 3358 Dihedral : 5.977 63.833 2743 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.05 % Allowed : 10.89 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.26 (0.18), residues: 2364 helix: 2.26 (0.14), residues: 1484 sheet: 0.59 (0.51), residues: 114 loop : 0.16 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 PHE 0.013 0.001 PHE B 549 TYR 0.012 0.001 TYR C 98 ARG 0.002 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 2.162 Fit side-chains REVERT: B 102 ASN cc_start: 0.6813 (m-40) cc_final: 0.6456 (m110) REVERT: C 639 ASN cc_start: 0.7720 (t0) cc_final: 0.7478 (t0) REVERT: C 644 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8498 (tt) REVERT: D 493 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6637 (mm-30) outliers start: 22 outliers final: 17 residues processed: 170 average time/residue: 0.2788 time to fit residues: 76.5605 Evaluate side-chains 164 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20158 Z= 0.238 Angle : 0.465 9.190 27322 Z= 0.237 Chirality : 0.037 0.168 3095 Planarity : 0.003 0.046 3358 Dihedral : 6.145 64.969 2743 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.95 % Allowed : 11.42 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.18 (0.18), residues: 2364 helix: 2.20 (0.14), residues: 1476 sheet: 0.65 (0.50), residues: 112 loop : 0.14 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 351 HIS 0.006 0.001 HIS A 269 PHE 0.017 0.001 PHE A 540 TYR 0.013 0.001 TYR C 98 ARG 0.003 0.000 ARG B 702 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 2.390 Fit side-chains REVERT: B 102 ASN cc_start: 0.6855 (m-40) cc_final: 0.6496 (m110) REVERT: C 644 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8508 (tt) REVERT: D 493 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6663 (mm-30) outliers start: 20 outliers final: 18 residues processed: 166 average time/residue: 0.2777 time to fit residues: 75.3127 Evaluate side-chains 165 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097018 restraints weight = 30108.187| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.60 r_work: 0.2989 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20158 Z= 0.135 Angle : 0.420 9.579 27322 Z= 0.217 Chirality : 0.035 0.184 3095 Planarity : 0.003 0.046 3358 Dihedral : 5.865 62.409 2743 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.95 % Allowed : 11.47 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.35 (0.18), residues: 2364 helix: 2.37 (0.14), residues: 1471 sheet: 0.61 (0.51), residues: 114 loop : 0.15 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.004 0.001 HIS A 269 PHE 0.013 0.001 PHE A 540 TYR 0.011 0.001 TYR C 98 ARG 0.002 0.000 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3398.40 seconds wall clock time: 64 minutes 45.18 seconds (3885.18 seconds total)