Starting phenix.real_space_refine on Sun Aug 24 11:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffl_29046/08_2025/8ffl_29046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffl_29046/08_2025/8ffl_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ffl_29046/08_2025/8ffl_29046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffl_29046/08_2025/8ffl_29046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ffl_29046/08_2025/8ffl_29046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffl_29046/08_2025/8ffl_29046.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'ARG:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 7, 'ARG:plan': 4, 'TRP:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 6, 'ARG:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 1, 'PHE: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: 4.26, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 650.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.64 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: 2.51 Time building geometry restraints manager: 1.51 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 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 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 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 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: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.790 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- 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= 0.114 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 : 3.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG D 100 TYR 0.013 0.001 TYR C 98 PHE 0.015 0.001 PHE C 429 TRP 0.014 0.001 TRP A 657 HIS 0.008 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00237 (20158) covalent geometry : angle 0.48892 (27322) hydrogen bonds : bond 0.14997 ( 1126) hydrogen bonds : angle 4.88157 ( 3228) *********************** 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 to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.475 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: 0.1065 time to fit residues: 25.9071 Evaluate side-chains 140 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094613 restraints weight = 30357.044| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.61 r_work: 0.2930 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20158 Z= 0.177 Angle : 0.495 6.371 27322 Z= 0.258 Chirality : 0.038 0.134 3095 Planarity : 0.004 0.040 3358 Dihedral : 7.123 66.440 2743 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.24 % Allowed : 7.09 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.18), residues: 2364 helix: 1.87 (0.14), residues: 1478 sheet: 0.88 (0.54), residues: 116 loop : 0.14 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.012 0.001 TYR C 515 PHE 0.020 0.001 PHE A 540 TRP 0.010 0.001 TRP A 657 HIS 0.008 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00428 (20158) covalent geometry : angle 0.49522 (27322) hydrogen bonds : bond 0.04278 ( 1126) hydrogen bonds : angle 4.05799 ( 3228) *********************** 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 178 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.939 Fit side-chains REVERT: A 540 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7444 (t80) REVERT: C 640 MET cc_start: 0.7792 (tpp) cc_final: 0.7416 (mmt) REVERT: C 644 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 645 MET cc_start: 0.7455 (mtt) cc_final: 0.7212 (mtp) outliers start: 26 outliers final: 11 residues processed: 172 average time/residue: 0.1134 time to fit residues: 31.7786 Evaluate side-chains 153 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 540 PHE 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 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 D residue 522 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 76 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094711 restraints weight = 30603.477| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.63 r_work: 0.2855 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20158 Z= 0.152 Angle : 0.462 6.494 27322 Z= 0.240 Chirality : 0.037 0.161 3095 Planarity : 0.004 0.042 3358 Dihedral : 7.029 64.143 2743 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.14 % Allowed : 8.18 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.18), residues: 2364 helix: 1.93 (0.14), residues: 1485 sheet: 0.69 (0.52), residues: 116 loop : 0.06 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 702 TYR 0.011 0.001 TYR A 544 PHE 0.018 0.001 PHE A 540 TRP 0.011 0.001 TRP D 333 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00370 (20158) covalent geometry : angle 0.46232 (27322) hydrogen bonds : bond 0.03725 ( 1126) hydrogen bonds : angle 3.88378 ( 3228) *********************** 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 176 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.685 Fit side-chains REVERT: C 519 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7307 (p90) REVERT: C 640 MET cc_start: 0.7923 (tpp) cc_final: 0.7559 (mtt) REVERT: C 644 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8408 (tt) REVERT: C 645 MET cc_start: 0.7408 (mtt) cc_final: 0.7161 (mtm) REVERT: D 493 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6668 (mm-30) outliers start: 24 outliers final: 11 residues processed: 169 average time/residue: 0.1184 time to fit residues: 33.1167 Evaluate side-chains 157 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 B residue 644 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 27 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 120 optimal weight: 0.4980 chunk 187 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.113298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.090819 restraints weight = 30946.836| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.61 r_work: 0.2882 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 20158 Z= 0.306 Angle : 0.604 8.019 27322 Z= 0.308 Chirality : 0.042 0.190 3095 Planarity : 0.004 0.047 3358 Dihedral : 7.397 59.928 2743 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.62 % Allowed : 9.66 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.17), residues: 2364 helix: 1.58 (0.14), residues: 1487 sheet: 0.40 (0.51), residues: 116 loop : -0.15 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 702 TYR 0.019 0.002 TYR D 471 PHE 0.026 0.002 PHE A 540 TRP 0.013 0.002 TRP D 333 HIS 0.008 0.002 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00753 (20158) covalent geometry : angle 0.60376 (27322) hydrogen bonds : bond 0.04468 ( 1126) hydrogen bonds : angle 4.10044 ( 3228) *********************** 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 175 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.800 Fit side-chains REVERT: C 182 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8113 (tt) REVERT: C 519 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7360 (p90) REVERT: C 644 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8607 (tt) REVERT: C 645 MET cc_start: 0.7430 (mtt) cc_final: 0.7182 (mtm) REVERT: D 493 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6746 (mm-30) outliers start: 34 outliers final: 16 residues processed: 168 average time/residue: 0.1175 time to fit residues: 32.7225 Evaluate side-chains 155 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 644 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 B residue 644 LEU 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 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 204 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094076 restraints weight = 30356.688| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.56 r_work: 0.2943 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20158 Z= 0.116 Angle : 0.446 7.154 27322 Z= 0.232 Chirality : 0.036 0.150 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.992 64.696 2743 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.28 % Allowed : 10.09 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.18), residues: 2364 helix: 1.96 (0.14), residues: 1474 sheet: 0.44 (0.50), residues: 114 loop : -0.09 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 100 TYR 0.013 0.001 TYR C 98 PHE 0.019 0.001 PHE A 540 TRP 0.013 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00273 (20158) covalent geometry : angle 0.44574 (27322) hydrogen bonds : bond 0.03475 ( 1126) hydrogen bonds : angle 3.81373 ( 3228) *********************** 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 174 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.920 Fit side-chains REVERT: B 128 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8474 (mp) REVERT: C 182 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8154 (tt) REVERT: C 639 ASN cc_start: 0.8106 (t0) cc_final: 0.7827 (t0) REVERT: C 644 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8592 (tt) REVERT: C 645 MET cc_start: 0.7464 (mtt) cc_final: 0.7223 (mtm) REVERT: C 650 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.7118 (t0) outliers start: 27 outliers final: 11 residues processed: 168 average time/residue: 0.1199 time to fit residues: 32.9602 Evaluate side-chains 155 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 128 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 182 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.117343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095074 restraints weight = 30325.747| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.63 r_work: 0.2947 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1281 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= 0.113 Angle : 0.432 8.090 27322 Z= 0.224 Chirality : 0.036 0.175 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.688 67.857 2743 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.38 % Allowed : 10.28 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.18), residues: 2364 helix: 2.08 (0.14), residues: 1483 sheet: 0.41 (0.50), residues: 114 loop : -0.01 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 100 TYR 0.011 0.001 TYR A 514 PHE 0.016 0.001 PHE A 540 TRP 0.010 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00271 (20158) covalent geometry : angle 0.43178 (27322) hydrogen bonds : bond 0.03298 ( 1126) hydrogen bonds : angle 3.73348 ( 3228) *********************** 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 178 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.826 Fit side-chains REVERT: C 173 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 519 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7330 (p90) REVERT: C 639 ASN cc_start: 0.8141 (t0) cc_final: 0.7801 (t0) REVERT: C 644 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8587 (tt) REVERT: C 645 MET cc_start: 0.7313 (mtt) cc_final: 0.7072 (mtm) REVERT: C 650 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.7108 (t0) REVERT: D 493 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6701 (mm-30) outliers start: 29 outliers final: 18 residues processed: 171 average time/residue: 0.1232 time to fit residues: 35.0970 Evaluate side-chains 169 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 528 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain B residue 645 MET 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 650 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 197 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.116772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.094411 restraints weight = 30504.639| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.60 r_work: 0.2944 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1346 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= 0.141 Angle : 0.454 9.255 27322 Z= 0.233 Chirality : 0.036 0.163 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.602 68.373 2743 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.38 % Allowed : 10.42 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.18), residues: 2364 helix: 2.06 (0.14), residues: 1482 sheet: 0.39 (0.50), residues: 114 loop : -0.01 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 702 TYR 0.013 0.001 TYR C 98 PHE 0.017 0.001 PHE A 540 TRP 0.009 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00343 (20158) covalent geometry : angle 0.45363 (27322) hydrogen bonds : bond 0.03390 ( 1126) hydrogen bonds : angle 3.72618 ( 3228) *********************** 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 182 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.624 Fit side-chains REVERT: B 102 ASN cc_start: 0.6766 (m-40) cc_final: 0.6351 (m110) REVERT: C 173 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 639 ASN cc_start: 0.7971 (t0) cc_final: 0.7704 (t0) REVERT: C 644 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8549 (tt) REVERT: C 645 MET cc_start: 0.7258 (mtt) cc_final: 0.7025 (mtm) REVERT: D 493 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6724 (mm-30) outliers start: 29 outliers final: 21 residues processed: 175 average time/residue: 0.1278 time to fit residues: 36.2839 Evaluate side-chains 170 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 159 ASP 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 671 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 200 optimal weight: 0.1980 chunk 58 optimal weight: 0.4980 chunk 219 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094508 restraints weight = 30344.019| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.63 r_work: 0.2949 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20158 Z= 0.128 Angle : 0.444 8.955 27322 Z= 0.228 Chirality : 0.036 0.158 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.472 67.816 2743 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.28 % Allowed : 10.85 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.18), residues: 2364 helix: 2.13 (0.14), residues: 1472 sheet: 0.43 (0.50), residues: 114 loop : 0.04 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 702 TYR 0.013 0.001 TYR C 98 PHE 0.016 0.001 PHE A 540 TRP 0.009 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00310 (20158) covalent geometry : angle 0.44376 (27322) hydrogen bonds : bond 0.03308 ( 1126) hydrogen bonds : angle 3.69919 ( 3228) *********************** 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 182 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.812 Fit side-chains REVERT: B 102 ASN cc_start: 0.6727 (m-40) cc_final: 0.6329 (m110) REVERT: C 173 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 644 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8563 (tt) REVERT: C 645 MET cc_start: 0.7279 (mtt) cc_final: 0.7053 (mtm) REVERT: D 493 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6603 (mm-30) outliers start: 27 outliers final: 20 residues processed: 176 average time/residue: 0.1357 time to fit residues: 38.7810 Evaluate side-chains 168 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 528 MET 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 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 159 ASP 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 671 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 131 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 180 optimal weight: 0.0870 chunk 195 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094350 restraints weight = 30168.203| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.52 r_work: 0.2950 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1425 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= 0.132 Angle : 0.451 9.291 27322 Z= 0.231 Chirality : 0.036 0.185 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.408 66.547 2743 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.28 % Allowed : 11.04 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.18), residues: 2364 helix: 2.14 (0.14), residues: 1472 sheet: 0.41 (0.50), residues: 114 loop : 0.04 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.012 0.001 TYR C 98 PHE 0.016 0.001 PHE A 540 TRP 0.009 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00320 (20158) covalent geometry : angle 0.45140 (27322) hydrogen bonds : bond 0.03310 ( 1126) hydrogen bonds : angle 3.68878 ( 3228) *********************** 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 174 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.803 Fit side-chains REVERT: B 102 ASN cc_start: 0.6872 (m-40) cc_final: 0.6441 (m110) REVERT: B 404 MET cc_start: 0.9047 (mmt) cc_final: 0.8565 (mmt) REVERT: C 173 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 644 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8589 (tt) REVERT: C 645 MET cc_start: 0.7281 (mtt) cc_final: 0.7060 (mtm) REVERT: D 493 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6624 (mm-30) outliers start: 27 outliers final: 18 residues processed: 168 average time/residue: 0.1201 time to fit residues: 33.2309 Evaluate side-chains 166 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 528 MET 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 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 159 ASP 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 671 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 0.0060 chunk 129 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.116642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094168 restraints weight = 30523.574| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.60 r_work: 0.2938 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1466 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= 0.151 Angle : 0.466 9.286 27322 Z= 0.238 Chirality : 0.037 0.175 3095 Planarity : 0.003 0.045 3358 Dihedral : 6.442 66.728 2743 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.14 % Allowed : 11.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2364 helix: 2.10 (0.14), residues: 1472 sheet: 0.52 (0.50), residues: 112 loop : 0.00 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 702 TYR 0.012 0.001 TYR C 98 PHE 0.017 0.001 PHE A 540 TRP 0.009 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00370 (20158) covalent geometry : angle 0.46561 (27322) hydrogen bonds : bond 0.03421 ( 1126) hydrogen bonds : angle 3.71255 ( 3228) ********************** 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 to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.615 Fit side-chains REVERT: A 193 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7677 (mtp-110) REVERT: B 102 ASN cc_start: 0.6901 (m-40) cc_final: 0.6457 (m110) REVERT: C 173 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7800 (tm-30) REVERT: C 644 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8562 (tt) REVERT: C 645 MET cc_start: 0.7259 (mtt) cc_final: 0.7043 (mtm) REVERT: D 493 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6546 (mm-30) outliers start: 24 outliers final: 19 residues processed: 162 average time/residue: 0.1151 time to fit residues: 30.4255 Evaluate side-chains 166 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 159 ASP 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 671 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 123 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.115764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093406 restraints weight = 30590.955| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.56 r_work: 0.2917 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20158 Z= 0.186 Angle : 0.496 9.373 27322 Z= 0.252 Chirality : 0.038 0.171 3095 Planarity : 0.004 0.045 3358 Dihedral : 6.577 68.253 2743 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.09 % Allowed : 11.37 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.18), residues: 2364 helix: 2.02 (0.14), residues: 1472 sheet: 0.48 (0.50), residues: 112 loop : -0.06 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 702 TYR 0.013 0.001 TYR C 98 PHE 0.020 0.001 PHE A 540 TRP 0.009 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00456 (20158) covalent geometry : angle 0.49564 (27322) hydrogen bonds : bond 0.03630 ( 1126) hydrogen bonds : angle 3.77077 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.89 seconds wall clock time: 64 minutes 40.79 seconds (3880.79 seconds total)