Starting phenix.real_space_refine on Wed Jun 11 01:49:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y04_33537/06_2025/7y04_33537.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y04_33537/06_2025/7y04_33537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y04_33537/06_2025/7y04_33537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y04_33537/06_2025/7y04_33537.map" model { file = "/net/cci-nas-00/data/ceres_data/7y04_33537/06_2025/7y04_33537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y04_33537/06_2025/7y04_33537.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 58 5.16 5 Be 2 3.05 5 C 7612 2.51 5 N 2041 2.21 5 O 2327 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12050 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5038 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 17, 'TRANS': 605} Chain breaks: 1 Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5021 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 17, 'TRANS': 603} Chain breaks: 1 Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 928 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 928 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "E" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 73 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.34, per 1000 atoms: 0.69 Number of scatterers: 12050 At special positions: 0 Unit cell: (107, 93.09, 136.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 4 15.00 F 6 9.00 O 2327 8.00 N 2041 7.00 C 7612 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2818 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 37.3% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 4.072A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 63 through 68 removed outlier: 4.231A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.828A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.797A pdb=" N TYR A 137 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.727A pdb=" N TYR A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.627A pdb=" N VAL A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 400 through 421 removed outlier: 3.744A pdb=" N ILE A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.811A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.642A pdb=" N VAL A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.353A pdb=" N TYR A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.596A pdb=" N LYS A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 571 Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.724A pdb=" N GLU A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 605 " --> pdb=" O ASN A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 removed outlier: 3.548A pdb=" N LEU A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 664 removed outlier: 4.098A pdb=" N VAL A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 689 removed outlier: 3.557A pdb=" N ARG A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 38 through 58 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.866A pdb=" N LEU B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.723A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 removed outlier: 3.743A pdb=" N TYR B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.640A pdb=" N TYR B 192 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.537A pdb=" N ILE B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 removed outlier: 3.544A pdb=" N SER B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 402 through 421 removed outlier: 3.868A pdb=" N LYS B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 removed outlier: 3.781A pdb=" N LYS B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 removed outlier: 4.189A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.583A pdb=" N SER B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 497 removed outlier: 3.699A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 removed outlier: 4.702A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 removed outlier: 4.165A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 560 Processing helix chain 'B' and resid 561 through 572 Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.745A pdb=" N ARG B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.757A pdb=" N GLN B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 removed outlier: 4.133A pdb=" N VAL B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 4.324A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 685 " --> pdb=" O TYR B 681 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 687 " --> pdb=" O MET B 683 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15 removed outlier: 3.861A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 165 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 183 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 84 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 83 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 78 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 85 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 76 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 214 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B 215 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU B 280 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 removed outlier: 4.036A pdb=" N GLU A 280 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 215 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 214 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 87 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 181 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 158 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 165 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 15 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 323 removed outlier: 3.844A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 329 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 363 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 513 removed outlier: 5.586A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.844A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 321 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 329 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 354 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 513 removed outlier: 5.664A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 68 removed outlier: 7.179A pdb=" N ASP C 63 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG C 78 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA C 6 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 30 removed outlier: 4.853A pdb=" N ASP C 26 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 41 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 68 removed outlier: 7.160A pdb=" N ASP D 63 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG D 78 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 74 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA D 6 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 24 through 31 removed outlier: 5.091A pdb=" N ASP D 26 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU D 41 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS D 49 " --> pdb=" O CYS D 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 47 " --> pdb=" O GLY D 42 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1152 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: 4.32 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2075 1.30 - 1.43: 3001 1.43 - 1.56: 7086 1.56 - 1.69: 10 1.69 - 1.81: 94 Bond restraints: 12266 Sorted by residual: bond pdb=" CA THR E 276 " pdb=" C THR E 276 " ideal model delta sigma weight residual 1.533 1.473 0.060 5.60e-03 3.19e+04 1.15e+02 bond pdb=" CA GLU A 13 " pdb=" CB GLU A 13 " ideal model delta sigma weight residual 1.530 1.448 0.082 1.48e-02 4.57e+03 3.08e+01 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N THR E 276 " pdb=" CA THR E 276 " ideal model delta sigma weight residual 1.457 1.425 0.032 6.40e-03 2.44e+04 2.48e+01 ... (remaining 12261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 16387 3.27 - 6.54: 92 6.54 - 9.81: 18 9.81 - 13.08: 6 13.08 - 16.34: 2 Bond angle restraints: 16505 Sorted by residual: angle pdb=" C THR E 276 " pdb=" CA THR E 276 " pdb=" CB THR E 276 " ideal model delta sigma weight residual 117.07 105.50 11.57 1.44e+00 4.82e-01 6.46e+01 angle pdb=" CA THR E 276 " pdb=" C THR E 276 " pdb=" N LYS E 277 " ideal model delta sigma weight residual 120.47 114.61 5.86 1.03e+00 9.43e-01 3.24e+01 angle pdb=" CA GLU A 13 " pdb=" C GLU A 13 " pdb=" N THR A 14 " ideal model delta sigma weight residual 115.86 122.91 -7.05 1.24e+00 6.50e-01 3.23e+01 angle pdb=" PA ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sigma weight residual 120.50 136.84 -16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" PA ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sigma weight residual 120.50 136.80 -16.30 3.00e+00 1.11e-01 2.95e+01 ... (remaining 16500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 7251 30.40 - 60.81: 244 60.81 - 91.21: 27 91.21 - 121.62: 1 121.62 - 152.02: 3 Dihedral angle restraints: 7526 sinusoidal: 3190 harmonic: 4336 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 147.98 152.02 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 149.00 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 173.79 126.21 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 7523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1396 0.047 - 0.095: 312 0.095 - 0.142: 92 0.142 - 0.189: 11 0.189 - 0.236: 1 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA GLU E 273 " pdb=" N GLU E 273 " pdb=" C GLU E 273 " pdb=" CB GLU E 273 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 392 " pdb=" N ARG A 392 " pdb=" C ARG A 392 " pdb=" CB ARG A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA GLU B 418 " pdb=" N GLU B 418 " pdb=" C GLU B 418 " pdb=" CB GLU B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1809 not shown) Planarity restraints: 2105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 272 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C LEU E 272 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU E 272 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU E 273 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 274 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C ILE E 274 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE E 274 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG E 275 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 276 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C THR E 276 " 0.034 2.00e-02 2.50e+03 pdb=" O THR E 276 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS E 277 " -0.011 2.00e-02 2.50e+03 ... (remaining 2102 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1398 2.75 - 3.29: 11492 3.29 - 3.83: 17824 3.83 - 4.36: 21066 4.36 - 4.90: 37507 Nonbonded interactions: 89287 Sorted by model distance: nonbonded pdb=" OH TYR B 56 " pdb=" OE1 GLN B 118 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLU A 548 " pdb=" NZ LYS A 551 " model vdw 2.221 3.120 nonbonded pdb=" O ILE B 353 " pdb=" OG SER B 365 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 457 " pdb=" OD1 ASP A 518 " model vdw 2.249 3.040 nonbonded pdb=" NZ LYS A 199 " pdb=" OE2 GLU A 280 " model vdw 2.275 3.120 ... (remaining 89282 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 10 through 217 or resid 278 through 690 or resid 801 throu \ gh 802)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 32.570 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 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 : 0.010 0.693 12268 Z= 0.907 Angle : 0.763 16.344 16505 Z= 0.397 Chirality : 0.044 0.236 1812 Planarity : 0.004 0.049 2105 Dihedral : 15.694 152.020 4708 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.75 % Allowed : 0.37 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.21), residues: 1461 helix: -0.78 (0.23), residues: 489 sheet: -2.78 (0.27), residues: 294 loop : -1.83 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 157 HIS 0.006 0.001 HIS D 57 PHE 0.013 0.001 PHE C 38 TYR 0.012 0.001 TYR A 681 ARG 0.007 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.22018 ( 427) hydrogen bonds : angle 8.09700 ( 1152) covalent geometry : bond 0.00426 (12266) covalent geometry : angle 0.76275 (16505) Misc. bond : bond 0.68185 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 1.408 Fit side-chains REVERT: A 280 GLU cc_start: 0.7466 (tt0) cc_final: 0.7220 (pt0) REVERT: A 372 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 546 ASP cc_start: 0.7582 (t70) cc_final: 0.7018 (t70) REVERT: A 550 LYS cc_start: 0.7535 (mptt) cc_final: 0.7215 (mmtt) REVERT: A 577 LYS cc_start: 0.7619 (ptmm) cc_final: 0.7231 (ptpp) REVERT: A 629 ASN cc_start: 0.8596 (t0) cc_final: 0.8238 (t0) REVERT: B 11 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5139 (pm20) REVERT: B 552 LYS cc_start: 0.8410 (tmtt) cc_final: 0.8185 (tptt) REVERT: B 553 MET cc_start: 0.9073 (tmm) cc_final: 0.8715 (tmm) REVERT: B 573 LYS cc_start: 0.8711 (tppt) cc_final: 0.8152 (ttpp) REVERT: B 629 ASN cc_start: 0.8856 (t0) cc_final: 0.8620 (t0) REVERT: C 47 PHE cc_start: 0.6818 (m-80) cc_final: 0.6386 (m-10) REVERT: C 104 ASN cc_start: 0.8057 (m-40) cc_final: 0.7844 (m-40) REVERT: D 37 THR cc_start: 0.7093 (t) cc_final: 0.6751 (p) REVERT: D 81 GLU cc_start: 0.7428 (mp0) cc_final: 0.6999 (mp0) REVERT: E 273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: E 275 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6710 (tmt170) outliers start: 10 outliers final: 1 residues processed: 203 average time/residue: 0.2986 time to fit residues: 83.2412 Evaluate side-chains 162 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN B 100 ASN C 57 HIS C 84 GLN D 57 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113412 restraints weight = 14864.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120048 restraints weight = 8791.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123411 restraints weight = 4850.415| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12268 Z= 0.166 Angle : 0.635 7.660 16505 Z= 0.324 Chirality : 0.044 0.169 1812 Planarity : 0.004 0.042 2105 Dihedral : 8.876 151.790 1626 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.34 % Allowed : 8.07 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.21), residues: 1461 helix: -0.34 (0.24), residues: 496 sheet: -2.18 (0.29), residues: 298 loop : -1.78 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 157 HIS 0.004 0.001 HIS B 149 PHE 0.013 0.001 PHE D 38 TYR 0.014 0.001 TYR A 305 ARG 0.008 0.001 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 427) hydrogen bonds : angle 5.65093 ( 1152) covalent geometry : bond 0.00390 (12266) covalent geometry : angle 0.63534 (16505) Misc. bond : bond 0.00251 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.607 Fit side-chains REVERT: A 11 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6238 (pm20) REVERT: A 501 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 546 ASP cc_start: 0.8012 (t70) cc_final: 0.7234 (t70) REVERT: A 550 LYS cc_start: 0.8042 (mptt) cc_final: 0.7528 (mmtt) REVERT: A 577 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7697 (ptpp) REVERT: A 629 ASN cc_start: 0.8895 (t0) cc_final: 0.8552 (t0) REVERT: A 652 LYS cc_start: 0.8166 (mttp) cc_final: 0.7966 (mttp) REVERT: B 100 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.7056 (t0) REVERT: B 424 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 471 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6672 (mt-10) REVERT: B 553 MET cc_start: 0.9190 (tmm) cc_final: 0.8760 (tmm) REVERT: B 573 LYS cc_start: 0.8619 (tppt) cc_final: 0.8126 (ttpp) REVERT: B 629 ASN cc_start: 0.9067 (t0) cc_final: 0.8848 (t0) REVERT: C 9 TYR cc_start: 0.6801 (p90) cc_final: 0.6333 (p90) REVERT: C 47 PHE cc_start: 0.7361 (m-80) cc_final: 0.6939 (m-10) REVERT: D 37 THR cc_start: 0.7356 (t) cc_final: 0.7006 (p) REVERT: D 81 GLU cc_start: 0.7850 (mp0) cc_final: 0.7331 (mp0) outliers start: 18 outliers final: 9 residues processed: 173 average time/residue: 0.3682 time to fit residues: 89.8222 Evaluate side-chains 156 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 119 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126280 restraints weight = 14387.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130964 restraints weight = 9870.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131953 restraints weight = 6689.708| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12268 Z= 0.136 Angle : 0.581 7.574 16505 Z= 0.296 Chirality : 0.043 0.157 1812 Planarity : 0.003 0.040 2105 Dihedral : 7.955 146.034 1622 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.57 % Allowed : 10.60 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1461 helix: -0.12 (0.24), residues: 499 sheet: -1.90 (0.29), residues: 298 loop : -1.77 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 157 HIS 0.004 0.001 HIS B 149 PHE 0.011 0.001 PHE D 38 TYR 0.012 0.001 TYR A 305 ARG 0.005 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 427) hydrogen bonds : angle 5.26004 ( 1152) covalent geometry : bond 0.00317 (12266) covalent geometry : angle 0.58097 (16505) Misc. bond : bond 0.00145 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 2.104 Fit side-chains revert: symmetry clash REVERT: A 546 ASP cc_start: 0.7961 (t70) cc_final: 0.7319 (t70) REVERT: A 550 LYS cc_start: 0.8224 (mptt) cc_final: 0.7744 (mmtt) REVERT: A 652 LYS cc_start: 0.8346 (mttp) cc_final: 0.8107 (mttp) REVERT: B 100 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7546 (t0) REVERT: B 553 MET cc_start: 0.8854 (tmm) cc_final: 0.8559 (tmm) REVERT: B 573 LYS cc_start: 0.8331 (tppt) cc_final: 0.8098 (ttpp) REVERT: B 581 SER cc_start: 0.6941 (m) cc_final: 0.6254 (m) REVERT: D 81 GLU cc_start: 0.8030 (mp0) cc_final: 0.7554 (mp0) REVERT: E 273 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: E 275 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6905 (tmt170) outliers start: 21 outliers final: 11 residues processed: 166 average time/residue: 0.3366 time to fit residues: 80.1048 Evaluate side-chains 156 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 128 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 108 optimal weight: 0.0040 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN B 100 ASN C 84 GLN D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.160298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128511 restraints weight = 14123.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132810 restraints weight = 9440.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136294 restraints weight = 6000.488| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12268 Z= 0.103 Angle : 0.542 6.893 16505 Z= 0.276 Chirality : 0.041 0.153 1812 Planarity : 0.003 0.038 2105 Dihedral : 7.732 178.879 1622 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.64 % Allowed : 11.73 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1461 helix: 0.06 (0.24), residues: 504 sheet: -1.64 (0.29), residues: 301 loop : -1.73 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 157 HIS 0.002 0.001 HIS A 625 PHE 0.008 0.001 PHE A 329 TYR 0.016 0.001 TYR C 9 ARG 0.006 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 427) hydrogen bonds : angle 4.94121 ( 1152) covalent geometry : bond 0.00231 (12266) covalent geometry : angle 0.54165 (16505) Misc. bond : bond 0.00083 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.378 Fit side-chains REVERT: A 550 LYS cc_start: 0.8391 (mptt) cc_final: 0.8178 (mptt) REVERT: A 594 SER cc_start: 0.8517 (t) cc_final: 0.8231 (t) REVERT: B 100 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7496 (t0) REVERT: B 418 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: B 553 MET cc_start: 0.9023 (tmm) cc_final: 0.8587 (tmm) REVERT: B 560 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7641 (t80) REVERT: D 81 GLU cc_start: 0.7944 (mp0) cc_final: 0.7478 (mp0) REVERT: E 275 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6860 (tmt170) outliers start: 22 outliers final: 12 residues processed: 170 average time/residue: 0.2863 time to fit residues: 68.7299 Evaluate side-chains 159 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 523 GLN B 100 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125394 restraints weight = 14338.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127744 restraints weight = 10692.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130231 restraints weight = 7864.474| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12268 Z= 0.153 Angle : 0.583 7.642 16505 Z= 0.295 Chirality : 0.043 0.170 1812 Planarity : 0.003 0.041 2105 Dihedral : 7.260 152.360 1619 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.02 % Allowed : 12.25 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1461 helix: 0.12 (0.24), residues: 496 sheet: -1.50 (0.29), residues: 298 loop : -1.70 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 157 HIS 0.004 0.001 HIS B 149 PHE 0.011 0.001 PHE D 38 TYR 0.011 0.001 TYR C 9 ARG 0.006 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 427) hydrogen bonds : angle 4.96060 ( 1152) covalent geometry : bond 0.00368 (12266) covalent geometry : angle 0.58264 (16505) Misc. bond : bond 0.00159 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 658 LEU cc_start: 0.7826 (tt) cc_final: 0.7546 (tp) REVERT: B 100 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7543 (t0) REVERT: B 418 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: B 453 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: B 553 MET cc_start: 0.8971 (tmm) cc_final: 0.8541 (tmm) REVERT: B 560 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7769 (t80) REVERT: B 573 LYS cc_start: 0.8581 (tppt) cc_final: 0.7975 (ttpp) REVERT: D 39 SER cc_start: 0.8243 (t) cc_final: 0.7506 (p) REVERT: D 81 GLU cc_start: 0.8014 (mp0) cc_final: 0.7527 (mp0) REVERT: E 275 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6889 (tmt170) outliers start: 27 outliers final: 14 residues processed: 163 average time/residue: 0.3048 time to fit residues: 69.6043 Evaluate side-chains 155 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain E residue 275 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 48 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 0.0170 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 133 optimal weight: 0.0870 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN B 100 ASN B 118 GLN D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118066 restraints weight = 14672.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121872 restraints weight = 10056.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124571 restraints weight = 6446.833| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12268 Z= 0.099 Angle : 0.542 7.271 16505 Z= 0.274 Chirality : 0.042 0.149 1812 Planarity : 0.003 0.037 2105 Dihedral : 6.430 110.829 1619 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.79 % Allowed : 12.85 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1461 helix: 0.38 (0.25), residues: 489 sheet: -1.33 (0.29), residues: 301 loop : -1.56 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 157 HIS 0.002 0.001 HIS A 625 PHE 0.008 0.001 PHE A 32 TYR 0.011 0.001 TYR C 9 ARG 0.006 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 427) hydrogen bonds : angle 4.74278 ( 1152) covalent geometry : bond 0.00225 (12266) covalent geometry : angle 0.54221 (16505) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.265 Fit side-chains REVERT: A 546 ASP cc_start: 0.7903 (t70) cc_final: 0.7218 (t0) REVERT: A 550 LYS cc_start: 0.8481 (mptt) cc_final: 0.8173 (mmtt) REVERT: A 594 SER cc_start: 0.8515 (t) cc_final: 0.8211 (t) REVERT: A 658 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7340 (tp) REVERT: B 25 MET cc_start: 0.7911 (tpp) cc_final: 0.7387 (mpp) REVERT: B 418 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: B 453 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: B 553 MET cc_start: 0.9055 (tmm) cc_final: 0.8557 (tmm) REVERT: B 560 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7656 (t80) REVERT: B 573 LYS cc_start: 0.8620 (tppt) cc_final: 0.8075 (ttpp) REVERT: D 39 SER cc_start: 0.8158 (t) cc_final: 0.7374 (p) outliers start: 24 outliers final: 15 residues processed: 162 average time/residue: 0.2669 time to fit residues: 61.5978 Evaluate side-chains 153 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain C residue 58 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 chunk 28 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.0570 chunk 95 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN B 100 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132879 restraints weight = 14007.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138574 restraints weight = 9279.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139663 restraints weight = 6071.271| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12268 Z= 0.097 Angle : 0.540 8.087 16505 Z= 0.272 Chirality : 0.041 0.163 1812 Planarity : 0.003 0.037 2105 Dihedral : 5.607 108.154 1615 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.87 % Allowed : 13.22 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1461 helix: 0.48 (0.25), residues: 489 sheet: -1.06 (0.30), residues: 306 loop : -1.47 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.002 0.001 HIS A 625 PHE 0.011 0.001 PHE C 16 TYR 0.026 0.001 TYR B 305 ARG 0.006 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 427) hydrogen bonds : angle 4.59214 ( 1152) covalent geometry : bond 0.00219 (12266) covalent geometry : angle 0.54021 (16505) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.406 Fit side-chains REVERT: A 546 ASP cc_start: 0.7851 (t70) cc_final: 0.7177 (t0) REVERT: A 550 LYS cc_start: 0.8508 (mptt) cc_final: 0.8219 (mmtt) REVERT: A 577 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7711 (ptpp) REVERT: A 594 SER cc_start: 0.8480 (t) cc_final: 0.8102 (t) REVERT: A 658 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7238 (tp) REVERT: B 25 MET cc_start: 0.7843 (tpp) cc_final: 0.7633 (tpp) REVERT: B 418 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: B 453 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: B 553 MET cc_start: 0.9097 (tmm) cc_final: 0.8568 (tmm) REVERT: B 560 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 573 LYS cc_start: 0.8751 (tppt) cc_final: 0.8201 (ttpp) REVERT: C 7 LYS cc_start: 0.7457 (mttt) cc_final: 0.7236 (mttm) REVERT: C 81 GLU cc_start: 0.7592 (mp0) cc_final: 0.7385 (mp0) REVERT: D 39 SER cc_start: 0.7980 (t) cc_final: 0.7195 (p) outliers start: 25 outliers final: 14 residues processed: 174 average time/residue: 0.2595 time to fit residues: 64.3035 Evaluate side-chains 165 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain C residue 58 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 0.0370 chunk 33 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130781 restraints weight = 14127.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136760 restraints weight = 9287.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137726 restraints weight = 5942.727| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12268 Z= 0.097 Angle : 0.538 6.974 16505 Z= 0.270 Chirality : 0.041 0.144 1812 Planarity : 0.003 0.063 2105 Dihedral : 5.438 105.551 1615 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.64 % Allowed : 13.59 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1461 helix: 0.50 (0.25), residues: 492 sheet: -0.88 (0.30), residues: 304 loop : -1.44 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 157 HIS 0.002 0.001 HIS B 149 PHE 0.007 0.001 PHE A 329 TYR 0.022 0.001 TYR B 305 ARG 0.005 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 427) hydrogen bonds : angle 4.57460 ( 1152) covalent geometry : bond 0.00223 (12266) covalent geometry : angle 0.53836 (16505) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.308 Fit side-chains REVERT: A 546 ASP cc_start: 0.7832 (t70) cc_final: 0.7089 (t0) REVERT: A 550 LYS cc_start: 0.8504 (mptt) cc_final: 0.8198 (mmtt) REVERT: A 577 LYS cc_start: 0.8044 (ptmm) cc_final: 0.7732 (ptpp) REVERT: A 594 SER cc_start: 0.8415 (t) cc_final: 0.8109 (t) REVERT: A 658 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7126 (tp) REVERT: B 25 MET cc_start: 0.7795 (tpp) cc_final: 0.7275 (mpp) REVERT: B 418 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: B 453 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: B 553 MET cc_start: 0.9086 (tmm) cc_final: 0.8556 (tmm) REVERT: B 560 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7631 (t80) REVERT: C 7 LYS cc_start: 0.7418 (mttt) cc_final: 0.7196 (mttm) REVERT: C 81 GLU cc_start: 0.7611 (mp0) cc_final: 0.7343 (mp0) REVERT: D 39 SER cc_start: 0.7966 (t) cc_final: 0.7185 (p) outliers start: 22 outliers final: 14 residues processed: 165 average time/residue: 0.2639 time to fit residues: 62.0282 Evaluate side-chains 161 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain C residue 58 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 125 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 132 optimal weight: 0.0070 chunk 3 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132102 restraints weight = 13940.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136576 restraints weight = 9700.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137724 restraints weight = 7102.151| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12268 Z= 0.112 Angle : 0.559 8.835 16505 Z= 0.280 Chirality : 0.042 0.143 1812 Planarity : 0.003 0.048 2105 Dihedral : 5.431 101.840 1615 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.64 % Allowed : 13.82 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1461 helix: 0.60 (0.25), residues: 484 sheet: -0.79 (0.30), residues: 301 loop : -1.39 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 157 HIS 0.003 0.001 HIS B 149 PHE 0.009 0.001 PHE C 16 TYR 0.021 0.001 TYR B 305 ARG 0.005 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 427) hydrogen bonds : angle 4.62713 ( 1152) covalent geometry : bond 0.00265 (12266) covalent geometry : angle 0.55915 (16505) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.307 Fit side-chains REVERT: A 546 ASP cc_start: 0.7805 (t70) cc_final: 0.7056 (t0) REVERT: A 550 LYS cc_start: 0.8457 (mptt) cc_final: 0.8106 (mmtt) REVERT: A 577 LYS cc_start: 0.8020 (ptmm) cc_final: 0.7717 (ptpp) REVERT: A 594 SER cc_start: 0.8446 (t) cc_final: 0.8124 (t) REVERT: A 658 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7114 (tp) REVERT: B 418 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: B 453 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: B 553 MET cc_start: 0.9115 (tmm) cc_final: 0.8577 (tmm) REVERT: B 560 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7559 (t80) REVERT: B 573 LYS cc_start: 0.8738 (tppt) cc_final: 0.8114 (ttpp) REVERT: C 7 LYS cc_start: 0.7419 (mttt) cc_final: 0.7166 (mttm) REVERT: C 81 GLU cc_start: 0.7609 (mp0) cc_final: 0.7336 (mp0) outliers start: 22 outliers final: 15 residues processed: 161 average time/residue: 0.2860 time to fit residues: 65.0775 Evaluate side-chains 164 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 96 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124232 restraints weight = 14267.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129726 restraints weight = 9702.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131100 restraints weight = 6200.907| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12268 Z= 0.105 Angle : 0.561 8.243 16505 Z= 0.279 Chirality : 0.042 0.165 1812 Planarity : 0.003 0.035 2105 Dihedral : 5.386 99.040 1615 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.57 % Allowed : 13.89 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1461 helix: 0.61 (0.25), residues: 485 sheet: -0.75 (0.30), residues: 306 loop : -1.33 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 157 HIS 0.003 0.001 HIS A 149 PHE 0.008 0.001 PHE C 16 TYR 0.021 0.001 TYR B 305 ARG 0.007 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 427) hydrogen bonds : angle 4.58354 ( 1152) covalent geometry : bond 0.00246 (12266) covalent geometry : angle 0.56063 (16505) Misc. bond : bond 0.00025 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 546 ASP cc_start: 0.7839 (t70) cc_final: 0.7089 (t0) REVERT: A 550 LYS cc_start: 0.8409 (mptt) cc_final: 0.8175 (mmtt) REVERT: A 577 LYS cc_start: 0.8057 (ptmm) cc_final: 0.7771 (ptpp) REVERT: A 594 SER cc_start: 0.8437 (t) cc_final: 0.8130 (t) REVERT: A 658 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7214 (tp) REVERT: B 418 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: B 453 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: B 553 MET cc_start: 0.9064 (tmm) cc_final: 0.8550 (tmm) REVERT: B 560 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 573 LYS cc_start: 0.8729 (tppt) cc_final: 0.8105 (ttpp) REVERT: C 7 LYS cc_start: 0.7513 (mttt) cc_final: 0.7240 (mttm) REVERT: C 81 GLU cc_start: 0.7608 (mp0) cc_final: 0.7370 (mp0) outliers start: 21 outliers final: 16 residues processed: 163 average time/residue: 0.2811 time to fit residues: 64.5721 Evaluate side-chains 164 residues out of total 1339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain D residue 57 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 126 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 397 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.161198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127916 restraints weight = 14037.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133112 restraints weight = 9699.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134217 restraints weight = 6679.311| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12268 Z= 0.175 Angle : 0.621 8.157 16505 Z= 0.311 Chirality : 0.044 0.182 1812 Planarity : 0.003 0.034 2105 Dihedral : 5.616 95.266 1615 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.64 % Allowed : 13.74 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1461 helix: 0.53 (0.25), residues: 481 sheet: -0.87 (0.30), residues: 304 loop : -1.39 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 157 HIS 0.005 0.001 HIS B 149 PHE 0.011 0.001 PHE A 32 TYR 0.020 0.001 TYR B 305 ARG 0.006 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 427) hydrogen bonds : angle 4.79226 ( 1152) covalent geometry : bond 0.00427 (12266) covalent geometry : angle 0.62050 (16505) Misc. bond : bond 0.00066 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.98 seconds wall clock time: 69 minutes 36.63 seconds (4176.63 seconds total)