Starting phenix.real_space_refine on Sun Apr 7 09:31:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl8_32577/04_2024/7wl8_32577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl8_32577/04_2024/7wl8_32577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl8_32577/04_2024/7wl8_32577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl8_32577/04_2024/7wl8_32577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl8_32577/04_2024/7wl8_32577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl8_32577/04_2024/7wl8_32577.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 5.57, per 1000 atoms: 0.55 Number of scatterers: 10198 At special positions: 0 Unit cell: (85.12, 127.68, 115.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 7 sheets defined 67.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.613A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.869A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.890A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 removed outlier: 5.132A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.018A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.598A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.592A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.752A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 348 Processing helix chain 'A' and resid 349 through 375 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.539A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.660A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.513A pdb=" N VAL A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.708A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.561A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.702A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.814A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.716A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.615A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.567A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.718A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.512A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.843A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.918A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.688A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.864A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.613A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.507A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 179 through 206 removed outlier: 3.628A pdb=" N LEU B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.597A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 214 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.793A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.742A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 375 removed outlier: 3.513A pdb=" N TYR B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.771A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.662A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.692A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.578A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.680A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.832A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.597A pdb=" N VAL B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.951A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.607A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.577A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.592A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.472A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.494A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 658 " --> pdb=" O TYR B 691 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 569 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3214 1.34 - 1.46: 2147 1.46 - 1.58: 4975 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" N LYS B 329 " pdb=" CA LYS B 329 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.89e-01 bond pdb=" CA ASP B 669 " pdb=" C ASP B 669 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.03e-01 bond pdb=" C TYR A 127 " pdb=" N PHE A 128 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 7.99e-01 bond pdb=" CA ASP A 669 " pdb=" C ASP A 669 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.21e-01 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.52e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.41: 299 107.41 - 114.06: 6172 114.06 - 120.71: 4380 120.71 - 127.36: 3210 127.36 - 134.01: 75 Bond angle restraints: 14136 Sorted by residual: angle pdb=" C ARG A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 120.62 125.21 -4.59 1.64e+00 3.72e-01 7.83e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.47 -4.50 1.80e+00 3.09e-01 6.24e+00 angle pdb=" C VAL A 97 " pdb=" N GLY A 98 " pdb=" CA GLY A 98 " ideal model delta sigma weight residual 120.00 122.58 -2.58 1.10e+00 8.26e-01 5.50e+00 angle pdb=" C VAL A 328 " pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 122.08 125.34 -3.26 1.47e+00 4.63e-01 4.93e+00 angle pdb=" C ASP B 669 " pdb=" N VAL B 670 " pdb=" CA VAL B 670 " ideal model delta sigma weight residual 121.97 125.93 -3.96 1.80e+00 3.09e-01 4.85e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5955 17.10 - 34.20: 183 34.20 - 51.29: 34 51.29 - 68.39: 6 68.39 - 85.49: 4 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" N LEU A 727 " pdb=" CA LEU A 727 " pdb=" CB LEU A 727 " pdb=" CG LEU A 727 " ideal model delta sinusoidal sigma weight residual -60.00 -119.14 59.14 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE A 385 " pdb=" CA PHE A 385 " pdb=" CB PHE A 385 " pdb=" CG PHE A 385 " ideal model delta sinusoidal sigma weight residual -60.00 -116.37 56.37 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 952 0.024 - 0.049: 440 0.049 - 0.073: 221 0.073 - 0.097: 78 0.097 - 0.122: 27 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA ILE B 331 " pdb=" N ILE B 331 " pdb=" C ILE B 331 " pdb=" CB ILE B 331 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO A 112 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 553 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO B 553 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.017 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2418 2.78 - 3.31: 10339 3.31 - 3.84: 16528 3.84 - 4.37: 19575 4.37 - 4.90: 33014 Nonbonded interactions: 81874 Sorted by model distance: nonbonded pdb=" OH TYR B 118 " pdb=" O GLY B 334 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.252 2.440 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.265 2.440 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.279 2.520 ... (remaining 81869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 6.970 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.100 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10400 Z= 0.116 Angle : 0.489 5.381 14136 Z= 0.299 Chirality : 0.037 0.122 1718 Planarity : 0.003 0.033 1758 Dihedral : 9.001 85.490 3710 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.87 % Allowed : 6.51 % Favored : 91.62 % 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: -3.89 (0.19), residues: 1322 helix: -2.31 (0.14), residues: 850 sheet: -2.48 (0.84), residues: 34 loop : -2.82 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 83 HIS 0.001 0.000 HIS B 656 PHE 0.007 0.001 PHE A 555 TYR 0.008 0.001 TYR A 377 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 335 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8676 (tt) cc_final: 0.8458 (tp) REVERT: A 145 SER cc_start: 0.8133 (m) cc_final: 0.7892 (p) REVERT: A 155 MET cc_start: 0.6791 (mpp) cc_final: 0.6328 (mpp) REVERT: A 237 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8549 (ttpp) REVERT: A 272 PHE cc_start: 0.8190 (t80) cc_final: 0.7901 (t80) REVERT: A 276 LEU cc_start: 0.8917 (mm) cc_final: 0.8417 (mm) REVERT: A 277 LEU cc_start: 0.8860 (mm) cc_final: 0.8438 (mt) REVERT: A 288 LEU cc_start: 0.8462 (tp) cc_final: 0.8250 (tp) REVERT: A 318 ASN cc_start: 0.7476 (t0) cc_final: 0.7241 (t0) REVERT: A 394 PHE cc_start: 0.8609 (t80) cc_final: 0.8393 (t80) REVERT: A 473 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8125 (mmmm) REVERT: A 477 THR cc_start: 0.8346 (p) cc_final: 0.7977 (t) REVERT: A 499 LEU cc_start: 0.8817 (tp) cc_final: 0.8525 (tt) REVERT: A 575 ILE cc_start: 0.8309 (mm) cc_final: 0.7098 (mm) REVERT: A 580 LYS cc_start: 0.7500 (tttt) cc_final: 0.6732 (tttp) REVERT: A 582 LEU cc_start: 0.8749 (mt) cc_final: 0.8234 (mp) REVERT: A 652 LYS cc_start: 0.6319 (pttt) cc_final: 0.6118 (pttm) REVERT: A 681 LYS cc_start: 0.8718 (tppt) cc_final: 0.8479 (tppp) REVERT: A 687 ASP cc_start: 0.8089 (t70) cc_final: 0.7721 (t0) REVERT: A 698 ASP cc_start: 0.7693 (t70) cc_final: 0.7352 (t0) REVERT: A 704 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6382 (tm-30) REVERT: A 706 CYS cc_start: 0.7633 (m) cc_final: 0.6372 (m) REVERT: B 66 LYS cc_start: 0.8414 (tptt) cc_final: 0.7971 (tppt) REVERT: B 157 PRO cc_start: 0.9182 (Cg_endo) cc_final: 0.8664 (Cg_exo) REVERT: B 161 PHE cc_start: 0.7927 (m-80) cc_final: 0.7621 (m-80) REVERT: B 210 PHE cc_start: 0.7891 (p90) cc_final: 0.7635 (p90) REVERT: B 276 LEU cc_start: 0.8957 (mm) cc_final: 0.8756 (tp) REVERT: B 277 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8618 (mm) REVERT: B 286 LYS cc_start: 0.8950 (tppt) cc_final: 0.8498 (tppt) REVERT: B 293 LYS cc_start: 0.8587 (tppt) cc_final: 0.8244 (tppt) REVERT: B 477 THR cc_start: 0.8501 (p) cc_final: 0.7894 (p) REVERT: B 486 CYS cc_start: 0.8379 (t) cc_final: 0.8159 (t) REVERT: B 496 LEU cc_start: 0.9104 (mm) cc_final: 0.8870 (mt) REVERT: B 580 LYS cc_start: 0.7844 (tttt) cc_final: 0.7305 (tttm) REVERT: B 583 LYS cc_start: 0.8405 (tmtt) cc_final: 0.8097 (tmtt) REVERT: B 668 LEU cc_start: 0.6839 (mt) cc_final: 0.6195 (mt) REVERT: B 670 VAL cc_start: 0.7689 (p) cc_final: 0.6898 (p) REVERT: B 698 ASP cc_start: 0.7684 (t70) cc_final: 0.7359 (t0) REVERT: B 701 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 704 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6377 (tm-30) REVERT: B 706 CYS cc_start: 0.7405 (m) cc_final: 0.6302 (m) REVERT: B 728 HIS cc_start: 0.8536 (t70) cc_final: 0.8328 (t-90) REVERT: B 731 ASN cc_start: 0.7033 (m-40) cc_final: 0.6826 (m-40) outliers start: 21 outliers final: 8 residues processed: 352 average time/residue: 0.3209 time to fit residues: 144.1675 Evaluate side-chains 277 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 268 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 77 optimal weight: 0.3980 chunk 119 optimal weight: 0.5980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 392 ASN A 421 GLN A 589 GLN A 656 HIS A 712 ASN A 730 GLN A 731 ASN ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN B 589 GLN B 656 HIS B 696 GLN B 712 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10400 Z= 0.179 Angle : 0.603 8.461 14136 Z= 0.305 Chirality : 0.042 0.167 1718 Planarity : 0.005 0.055 1758 Dihedral : 5.275 79.812 1433 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 2.23 % Allowed : 16.31 % Favored : 81.46 % 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: -1.80 (0.22), residues: 1322 helix: -0.38 (0.17), residues: 844 sheet: -3.02 (0.70), residues: 48 loop : -2.47 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 518 HIS 0.010 0.001 HIS B 656 PHE 0.018 0.001 PHE A 210 TYR 0.020 0.001 TYR A 377 ARG 0.018 0.001 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 280 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8704 (tt) cc_final: 0.8445 (tp) REVERT: A 155 MET cc_start: 0.6941 (mpp) cc_final: 0.6472 (mpp) REVERT: A 195 LEU cc_start: 0.8475 (tp) cc_final: 0.8252 (tt) REVERT: A 237 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8501 (ttpp) REVERT: A 272 PHE cc_start: 0.8250 (t80) cc_final: 0.7917 (t80) REVERT: A 276 LEU cc_start: 0.8934 (mm) cc_final: 0.8382 (mm) REVERT: A 277 LEU cc_start: 0.8875 (mm) cc_final: 0.8465 (mt) REVERT: A 283 MET cc_start: 0.7816 (mmm) cc_final: 0.7524 (mmm) REVERT: A 288 LEU cc_start: 0.8511 (tp) cc_final: 0.8266 (tp) REVERT: A 318 ASN cc_start: 0.7674 (t0) cc_final: 0.6988 (t0) REVERT: A 472 TRP cc_start: 0.8822 (t-100) cc_final: 0.8474 (t-100) REVERT: A 496 LEU cc_start: 0.9175 (mm) cc_final: 0.8959 (mt) REVERT: A 537 LYS cc_start: 0.8295 (tppt) cc_final: 0.8062 (tppt) REVERT: A 575 ILE cc_start: 0.8229 (mm) cc_final: 0.8023 (mm) REVERT: A 580 LYS cc_start: 0.7420 (tttt) cc_final: 0.6776 (tttm) REVERT: A 682 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7217 (mt-10) REVERT: A 685 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7517 (mtm110) REVERT: A 687 ASP cc_start: 0.8141 (t70) cc_final: 0.7768 (t0) REVERT: A 696 GLN cc_start: 0.6784 (mt0) cc_final: 0.6399 (mt0) REVERT: A 698 ASP cc_start: 0.7712 (t70) cc_final: 0.7333 (t0) REVERT: A 701 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7328 (mm-30) REVERT: B 39 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7408 (ttm-80) REVERT: B 66 LYS cc_start: 0.8565 (tptt) cc_final: 0.8223 (tppt) REVERT: B 77 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7903 (ttpp) REVERT: B 161 PHE cc_start: 0.7935 (m-80) cc_final: 0.7627 (m-80) REVERT: B 195 LEU cc_start: 0.8378 (tp) cc_final: 0.8112 (tt) REVERT: B 277 LEU cc_start: 0.9111 (mm) cc_final: 0.8759 (mm) REVERT: B 286 LYS cc_start: 0.9010 (tppt) cc_final: 0.8777 (tppp) REVERT: B 287 GLU cc_start: 0.7423 (pp20) cc_final: 0.7179 (pp20) REVERT: B 293 LYS cc_start: 0.8473 (tppt) cc_final: 0.8203 (tppt) REVERT: B 376 ASP cc_start: 0.7413 (t0) cc_final: 0.6927 (t0) REVERT: B 486 CYS cc_start: 0.8312 (t) cc_final: 0.8071 (t) REVERT: B 517 SER cc_start: 0.7715 (p) cc_final: 0.7402 (p) REVERT: B 549 ARG cc_start: 0.7626 (ttt180) cc_final: 0.7246 (ttt180) REVERT: B 573 ASP cc_start: 0.7256 (t0) cc_final: 0.6942 (t0) REVERT: B 579 ASN cc_start: 0.6585 (m110) cc_final: 0.6280 (m-40) REVERT: B 580 LYS cc_start: 0.7876 (tttt) cc_final: 0.7674 (tttp) REVERT: B 583 LYS cc_start: 0.8498 (tmtt) cc_final: 0.8200 (tmtt) REVERT: B 698 ASP cc_start: 0.7613 (t70) cc_final: 0.7248 (t0) REVERT: B 704 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6730 (tm-30) REVERT: B 728 HIS cc_start: 0.8514 (t70) cc_final: 0.8260 (t-170) outliers start: 25 outliers final: 10 residues processed: 299 average time/residue: 0.2893 time to fit residues: 114.0898 Evaluate side-chains 277 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 392 ASN ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 712 ASN A 731 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 728 HIS B 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10400 Z= 0.245 Angle : 0.613 10.042 14136 Z= 0.313 Chirality : 0.043 0.188 1718 Planarity : 0.004 0.040 1758 Dihedral : 5.284 79.711 1430 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.67 % Favored : 94.18 % Rotamer: Outliers : 3.30 % Allowed : 18.00 % Favored : 78.70 % 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: -0.96 (0.23), residues: 1322 helix: 0.29 (0.18), residues: 854 sheet: -1.59 (0.93), residues: 36 loop : -2.40 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 83 HIS 0.011 0.001 HIS B 656 PHE 0.022 0.001 PHE B 210 TYR 0.020 0.001 TYR A 377 ARG 0.011 0.001 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8745 (tt) cc_final: 0.8485 (tp) REVERT: A 134 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7872 (mmm-85) REVERT: A 272 PHE cc_start: 0.8412 (t80) cc_final: 0.8028 (t80) REVERT: A 276 LEU cc_start: 0.8984 (mm) cc_final: 0.8416 (mm) REVERT: A 283 MET cc_start: 0.7965 (mmm) cc_final: 0.7684 (mmm) REVERT: A 288 LEU cc_start: 0.8551 (tp) cc_final: 0.8310 (tp) REVERT: A 293 LYS cc_start: 0.8479 (tppt) cc_final: 0.8122 (tppt) REVERT: A 318 ASN cc_start: 0.7843 (t0) cc_final: 0.7611 (t0) REVERT: A 384 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 472 TRP cc_start: 0.8964 (t-100) cc_final: 0.8717 (t-100) REVERT: A 496 LEU cc_start: 0.9181 (mm) cc_final: 0.8933 (mt) REVERT: A 537 LYS cc_start: 0.8372 (tppt) cc_final: 0.8084 (mmtt) REVERT: A 580 LYS cc_start: 0.7411 (tttt) cc_final: 0.6709 (tttp) REVERT: A 687 ASP cc_start: 0.8161 (t70) cc_final: 0.7821 (t0) REVERT: A 696 GLN cc_start: 0.7012 (mt0) cc_final: 0.6750 (mt0) REVERT: A 698 ASP cc_start: 0.7775 (t70) cc_final: 0.7430 (t0) REVERT: B 66 LYS cc_start: 0.8543 (tptt) cc_final: 0.8194 (tppt) REVERT: B 77 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8040 (ttpp) REVERT: B 155 MET cc_start: 0.7226 (mpp) cc_final: 0.6795 (mpp) REVERT: B 195 LEU cc_start: 0.8405 (tp) cc_final: 0.8181 (tt) REVERT: B 277 LEU cc_start: 0.9154 (mm) cc_final: 0.8874 (mm) REVERT: B 286 LYS cc_start: 0.9048 (tppt) cc_final: 0.8814 (tppp) REVERT: B 293 LYS cc_start: 0.8529 (tppt) cc_final: 0.8183 (tppt) REVERT: B 320 GLU cc_start: 0.6691 (tm-30) cc_final: 0.6364 (tm-30) REVERT: B 376 ASP cc_start: 0.7417 (t0) cc_final: 0.6876 (t0) REVERT: B 384 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 486 CYS cc_start: 0.8297 (t) cc_final: 0.8060 (t) REVERT: B 517 SER cc_start: 0.7968 (p) cc_final: 0.7706 (p) REVERT: B 549 ARG cc_start: 0.7647 (ttt180) cc_final: 0.7264 (ttt180) REVERT: B 583 LYS cc_start: 0.8558 (tmtt) cc_final: 0.8239 (tmtt) REVERT: B 698 ASP cc_start: 0.7626 (t70) cc_final: 0.7277 (t0) REVERT: B 704 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6955 (tm-30) outliers start: 37 outliers final: 25 residues processed: 285 average time/residue: 0.2983 time to fit residues: 111.0239 Evaluate side-chains 270 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.0470 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 375 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 705 GLN B 731 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10400 Z= 0.202 Angle : 0.593 9.649 14136 Z= 0.302 Chirality : 0.042 0.165 1718 Planarity : 0.004 0.049 1758 Dihedral : 5.340 80.445 1430 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.33 % Rotamer: Outliers : 3.21 % Allowed : 20.41 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1322 helix: 0.55 (0.18), residues: 850 sheet: -1.03 (0.98), residues: 36 loop : -2.17 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 83 HIS 0.012 0.001 HIS B 656 PHE 0.024 0.001 PHE B 210 TYR 0.022 0.001 TYR A 377 ARG 0.010 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8752 (tt) cc_final: 0.8510 (tp) REVERT: A 134 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: A 195 LEU cc_start: 0.8482 (tp) cc_final: 0.8257 (tt) REVERT: A 236 LEU cc_start: 0.8799 (tp) cc_final: 0.8488 (tt) REVERT: A 272 PHE cc_start: 0.8429 (t80) cc_final: 0.8000 (t80) REVERT: A 276 LEU cc_start: 0.8981 (mm) cc_final: 0.8373 (mm) REVERT: A 283 MET cc_start: 0.8016 (mmm) cc_final: 0.7696 (mmm) REVERT: A 288 LEU cc_start: 0.8580 (tp) cc_final: 0.8330 (tp) REVERT: A 293 LYS cc_start: 0.8483 (tppt) cc_final: 0.8107 (tppt) REVERT: A 318 ASN cc_start: 0.7719 (t0) cc_final: 0.7507 (t0) REVERT: A 384 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 414 GLU cc_start: 0.7051 (tp30) cc_final: 0.6530 (tp30) REVERT: A 473 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8327 (mmmm) REVERT: A 496 LEU cc_start: 0.9151 (mm) cc_final: 0.8728 (mt) REVERT: A 518 TRP cc_start: 0.8541 (p-90) cc_final: 0.8026 (p-90) REVERT: A 580 LYS cc_start: 0.7454 (tttt) cc_final: 0.6849 (tttm) REVERT: A 682 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 687 ASP cc_start: 0.8177 (t70) cc_final: 0.7849 (t0) REVERT: A 696 GLN cc_start: 0.7040 (mt0) cc_final: 0.6796 (mt0) REVERT: A 698 ASP cc_start: 0.7774 (t70) cc_final: 0.7424 (t0) REVERT: A 712 ASN cc_start: 0.7925 (t0) cc_final: 0.7676 (t0) REVERT: B 29 GLU cc_start: 0.8073 (tp30) cc_final: 0.7733 (tp30) REVERT: B 66 LYS cc_start: 0.8535 (tptt) cc_final: 0.8169 (tppt) REVERT: B 77 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7832 (ttpp) REVERT: B 277 LEU cc_start: 0.9147 (mm) cc_final: 0.8884 (mm) REVERT: B 286 LYS cc_start: 0.9037 (tppt) cc_final: 0.8822 (tppp) REVERT: B 288 LEU cc_start: 0.8897 (tt) cc_final: 0.8501 (mm) REVERT: B 293 LYS cc_start: 0.8526 (tppt) cc_final: 0.8196 (tppt) REVERT: B 320 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6486 (tm-30) REVERT: B 369 LYS cc_start: 0.8823 (mttp) cc_final: 0.8618 (ttmm) REVERT: B 376 ASP cc_start: 0.7448 (t0) cc_final: 0.7111 (t70) REVERT: B 384 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7642 (mm-30) REVERT: B 486 CYS cc_start: 0.8238 (t) cc_final: 0.8033 (t) REVERT: B 517 SER cc_start: 0.7712 (p) cc_final: 0.7434 (p) REVERT: B 549 ARG cc_start: 0.7664 (ttt180) cc_final: 0.7315 (ttt180) REVERT: B 582 LEU cc_start: 0.8846 (mt) cc_final: 0.8627 (mp) REVERT: B 583 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8273 (tmtt) REVERT: B 587 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7228 (mmm-85) REVERT: B 698 ASP cc_start: 0.7627 (t70) cc_final: 0.7285 (t0) outliers start: 36 outliers final: 29 residues processed: 278 average time/residue: 0.2892 time to fit residues: 105.0334 Evaluate side-chains 273 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 244 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 731 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10400 Z= 0.232 Angle : 0.612 11.281 14136 Z= 0.312 Chirality : 0.043 0.172 1718 Planarity : 0.004 0.058 1758 Dihedral : 5.375 80.168 1430 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 4.19 % Allowed : 21.39 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1322 helix: 0.68 (0.18), residues: 850 sheet: -0.99 (0.93), residues: 36 loop : -2.07 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 83 HIS 0.010 0.001 HIS B 656 PHE 0.029 0.001 PHE A 210 TYR 0.018 0.001 TYR A 578 ARG 0.011 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8779 (tt) cc_final: 0.8546 (tp) REVERT: A 155 MET cc_start: 0.7080 (mpp) cc_final: 0.6678 (mpp) REVERT: A 259 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 272 PHE cc_start: 0.8460 (t80) cc_final: 0.8046 (t80) REVERT: A 276 LEU cc_start: 0.8992 (mm) cc_final: 0.8399 (mm) REVERT: A 283 MET cc_start: 0.8058 (mmm) cc_final: 0.7720 (mmm) REVERT: A 288 LEU cc_start: 0.8609 (tp) cc_final: 0.8364 (tp) REVERT: A 293 LYS cc_start: 0.8494 (tppt) cc_final: 0.8113 (tppt) REVERT: A 384 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 472 TRP cc_start: 0.8976 (t-100) cc_final: 0.8470 (t-100) REVERT: A 496 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 537 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8213 (mmtt) REVERT: A 580 LYS cc_start: 0.7455 (tttt) cc_final: 0.6911 (tttm) REVERT: A 687 ASP cc_start: 0.8183 (t70) cc_final: 0.7860 (t0) REVERT: A 696 GLN cc_start: 0.7133 (mt0) cc_final: 0.6917 (mt0) REVERT: A 698 ASP cc_start: 0.7761 (t70) cc_final: 0.7434 (t0) REVERT: A 712 ASN cc_start: 0.7959 (t0) cc_final: 0.7703 (t0) REVERT: B 66 LYS cc_start: 0.8560 (tptt) cc_final: 0.8329 (tptp) REVERT: B 277 LEU cc_start: 0.9152 (mm) cc_final: 0.8887 (mm) REVERT: B 286 LYS cc_start: 0.9031 (tppt) cc_final: 0.8829 (tppp) REVERT: B 288 LEU cc_start: 0.8903 (tt) cc_final: 0.8501 (mm) REVERT: B 293 LYS cc_start: 0.8554 (tppt) cc_final: 0.8199 (tppt) REVERT: B 320 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6494 (tm-30) REVERT: B 376 ASP cc_start: 0.7407 (t0) cc_final: 0.7078 (t70) REVERT: B 384 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 486 CYS cc_start: 0.8270 (t) cc_final: 0.8035 (t) REVERT: B 517 SER cc_start: 0.7797 (p) cc_final: 0.7518 (p) REVERT: B 549 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7361 (ttt180) REVERT: B 583 LYS cc_start: 0.8571 (tmtt) cc_final: 0.8289 (tmtt) REVERT: B 587 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7024 (mmm-85) REVERT: B 698 ASP cc_start: 0.7644 (t70) cc_final: 0.7305 (t0) outliers start: 47 outliers final: 35 residues processed: 282 average time/residue: 0.2794 time to fit residues: 104.1153 Evaluate side-chains 282 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 34 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 382 ASN B 656 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10400 Z= 0.336 Angle : 0.675 13.614 14136 Z= 0.347 Chirality : 0.045 0.181 1718 Planarity : 0.005 0.056 1758 Dihedral : 5.510 79.728 1428 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 4.10 % Allowed : 23.08 % Favored : 72.82 % 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: -0.29 (0.24), residues: 1322 helix: 0.68 (0.18), residues: 860 sheet: -0.69 (0.93), residues: 36 loop : -1.93 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 83 HIS 0.014 0.001 HIS B 656 PHE 0.024 0.002 PHE A 210 TYR 0.021 0.002 TYR B 377 ARG 0.014 0.001 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 254 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8897 (tt) cc_final: 0.8663 (tp) REVERT: A 155 MET cc_start: 0.7273 (mpp) cc_final: 0.6698 (mpp) REVERT: A 272 PHE cc_start: 0.8516 (t80) cc_final: 0.8042 (t80) REVERT: A 276 LEU cc_start: 0.9012 (mm) cc_final: 0.8387 (mm) REVERT: A 283 MET cc_start: 0.8084 (mmm) cc_final: 0.7745 (mmm) REVERT: A 288 LEU cc_start: 0.8866 (tp) cc_final: 0.8597 (tp) REVERT: A 293 LYS cc_start: 0.8536 (tppt) cc_final: 0.8129 (tppt) REVERT: A 369 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8433 (mtmm) REVERT: A 374 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8342 (ttmm) REVERT: A 496 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8480 (mt) REVERT: A 537 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8028 (mmmt) REVERT: A 580 LYS cc_start: 0.7375 (tttt) cc_final: 0.6819 (tttm) REVERT: A 681 LYS cc_start: 0.8814 (tppp) cc_final: 0.8522 (tppp) REVERT: A 687 ASP cc_start: 0.8207 (t70) cc_final: 0.7879 (t0) REVERT: A 698 ASP cc_start: 0.7795 (t70) cc_final: 0.7484 (t0) REVERT: A 704 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 712 ASN cc_start: 0.7977 (t0) cc_final: 0.7652 (t0) REVERT: B 66 LYS cc_start: 0.8558 (tptt) cc_final: 0.8253 (tptp) REVERT: B 288 LEU cc_start: 0.8914 (tt) cc_final: 0.8500 (mm) REVERT: B 293 LYS cc_start: 0.8622 (tppt) cc_final: 0.8235 (tppt) REVERT: B 320 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6695 (tm-30) REVERT: B 384 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 486 CYS cc_start: 0.8304 (t) cc_final: 0.8073 (t) REVERT: B 496 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9024 (mt) REVERT: B 549 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7343 (ttt180) REVERT: B 583 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8180 (tmmt) REVERT: B 698 ASP cc_start: 0.7677 (t70) cc_final: 0.7338 (t0) outliers start: 46 outliers final: 31 residues processed: 277 average time/residue: 0.2856 time to fit residues: 104.3462 Evaluate side-chains 274 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 240 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 730 GLN A 731 ASN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN B 656 HIS B 705 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10400 Z= 0.249 Angle : 0.655 13.374 14136 Z= 0.334 Chirality : 0.044 0.184 1718 Planarity : 0.004 0.043 1758 Dihedral : 5.526 80.965 1428 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 4.28 % Allowed : 22.91 % Favored : 72.82 % 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: -0.13 (0.24), residues: 1322 helix: 0.77 (0.18), residues: 862 sheet: -0.54 (0.96), residues: 36 loop : -1.79 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 83 HIS 0.015 0.001 HIS B 656 PHE 0.028 0.001 PHE B 210 TYR 0.025 0.001 TYR B 377 ARG 0.011 0.001 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 244 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8845 (tt) cc_final: 0.8610 (tp) REVERT: A 155 MET cc_start: 0.7308 (mpp) cc_final: 0.6655 (mpp) REVERT: A 272 PHE cc_start: 0.8491 (t80) cc_final: 0.8024 (t80) REVERT: A 276 LEU cc_start: 0.9012 (mm) cc_final: 0.8387 (mm) REVERT: A 283 MET cc_start: 0.8087 (mmm) cc_final: 0.7731 (mmm) REVERT: A 288 LEU cc_start: 0.8860 (tp) cc_final: 0.8588 (tp) REVERT: A 293 LYS cc_start: 0.8523 (tppt) cc_final: 0.8110 (tppt) REVERT: A 369 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8366 (mtmt) REVERT: A 496 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8847 (mt) REVERT: A 537 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8041 (mmmt) REVERT: A 580 LYS cc_start: 0.7360 (tttt) cc_final: 0.6559 (tttp) REVERT: A 681 LYS cc_start: 0.8789 (tppp) cc_final: 0.8493 (tppp) REVERT: A 687 ASP cc_start: 0.8203 (t70) cc_final: 0.7879 (t0) REVERT: A 698 ASP cc_start: 0.7800 (t70) cc_final: 0.7511 (t0) REVERT: A 704 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 712 ASN cc_start: 0.7974 (t0) cc_final: 0.7639 (t0) REVERT: B 66 LYS cc_start: 0.8570 (tptt) cc_final: 0.8259 (tptp) REVERT: B 213 ARG cc_start: 0.7398 (mtt90) cc_final: 0.6869 (mtt-85) REVERT: B 287 GLU cc_start: 0.7370 (pp20) cc_final: 0.6739 (pp20) REVERT: B 288 LEU cc_start: 0.8900 (tt) cc_final: 0.8175 (mm) REVERT: B 293 LYS cc_start: 0.8627 (tppt) cc_final: 0.8219 (tppt) REVERT: B 320 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 376 ASP cc_start: 0.7475 (t0) cc_final: 0.6877 (t70) REVERT: B 472 TRP cc_start: 0.8929 (t-100) cc_final: 0.8499 (t-100) REVERT: B 486 CYS cc_start: 0.8294 (t) cc_final: 0.8065 (t) REVERT: B 583 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8297 (tmtt) REVERT: B 698 ASP cc_start: 0.7679 (t70) cc_final: 0.7310 (t0) outliers start: 48 outliers final: 35 residues processed: 266 average time/residue: 0.2948 time to fit residues: 103.9982 Evaluate side-chains 272 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.0170 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 730 GLN A 731 ASN B 207 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 656 HIS B 705 GLN B 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10400 Z= 0.202 Angle : 0.649 12.350 14136 Z= 0.328 Chirality : 0.042 0.178 1718 Planarity : 0.004 0.068 1758 Dihedral : 5.011 80.691 1425 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.02 % Rotamer: Outliers : 3.39 % Allowed : 23.89 % Favored : 72.73 % 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: -0.02 (0.24), residues: 1322 helix: 0.83 (0.18), residues: 864 sheet: -0.27 (1.01), residues: 36 loop : -1.73 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 83 HIS 0.015 0.001 HIS B 656 PHE 0.029 0.001 PHE B 210 TYR 0.032 0.001 TYR B 377 ARG 0.011 0.001 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8872 (tt) cc_final: 0.8633 (tp) REVERT: A 155 MET cc_start: 0.7332 (mpp) cc_final: 0.6620 (mpp) REVERT: A 236 LEU cc_start: 0.8847 (tp) cc_final: 0.8498 (tt) REVERT: A 272 PHE cc_start: 0.8474 (t80) cc_final: 0.8036 (t80) REVERT: A 276 LEU cc_start: 0.8987 (mm) cc_final: 0.8374 (mm) REVERT: A 283 MET cc_start: 0.8046 (mmm) cc_final: 0.7781 (mmm) REVERT: A 288 LEU cc_start: 0.8843 (tp) cc_final: 0.8575 (tp) REVERT: A 293 LYS cc_start: 0.8434 (tppt) cc_final: 0.8008 (tppt) REVERT: A 369 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8291 (mtmt) REVERT: A 472 TRP cc_start: 0.9019 (t-100) cc_final: 0.8619 (t-100) REVERT: A 496 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8832 (mt) REVERT: A 537 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8034 (mmmt) REVERT: A 580 LYS cc_start: 0.7236 (tttt) cc_final: 0.6651 (tttp) REVERT: A 687 ASP cc_start: 0.8165 (t70) cc_final: 0.7842 (t0) REVERT: A 698 ASP cc_start: 0.7784 (t70) cc_final: 0.7499 (t0) REVERT: A 704 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 712 ASN cc_start: 0.7993 (t0) cc_final: 0.7743 (t0) REVERT: B 66 LYS cc_start: 0.8546 (tptt) cc_final: 0.8238 (tptp) REVERT: B 255 TYR cc_start: 0.8356 (m-10) cc_final: 0.7860 (m-10) REVERT: B 288 LEU cc_start: 0.8886 (tt) cc_final: 0.8476 (mm) REVERT: B 293 LYS cc_start: 0.8588 (tppt) cc_final: 0.8163 (tppt) REVERT: B 320 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6553 (tm-30) REVERT: B 486 CYS cc_start: 0.8234 (t) cc_final: 0.8023 (t) REVERT: B 517 SER cc_start: 0.7706 (p) cc_final: 0.7428 (p) REVERT: B 549 ARG cc_start: 0.7736 (ttt180) cc_final: 0.7517 (ttt180) REVERT: B 583 LYS cc_start: 0.8569 (tmtt) cc_final: 0.8301 (tmtt) REVERT: B 698 ASP cc_start: 0.7646 (t70) cc_final: 0.7294 (t0) outliers start: 38 outliers final: 28 residues processed: 262 average time/residue: 0.2872 time to fit residues: 98.7235 Evaluate side-chains 268 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 HIS Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 93 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.0170 chunk 76 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 730 GLN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 696 GLN B 705 GLN B 731 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10400 Z= 0.214 Angle : 0.677 14.499 14136 Z= 0.341 Chirality : 0.043 0.182 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.019 80.144 1423 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 3.03 % Allowed : 24.60 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1322 helix: 0.90 (0.18), residues: 862 sheet: -0.22 (1.00), residues: 36 loop : -1.66 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 83 HIS 0.021 0.002 HIS B 656 PHE 0.031 0.001 PHE B 210 TYR 0.032 0.001 TYR B 377 ARG 0.010 0.001 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 238 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8878 (tt) cc_final: 0.8647 (tp) REVERT: A 236 LEU cc_start: 0.8849 (tp) cc_final: 0.8515 (tt) REVERT: A 266 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6816 (p0) REVERT: A 272 PHE cc_start: 0.8495 (t80) cc_final: 0.8031 (t80) REVERT: A 276 LEU cc_start: 0.8993 (mm) cc_final: 0.8372 (mm) REVERT: A 283 MET cc_start: 0.8057 (mmm) cc_final: 0.7804 (mmm) REVERT: A 288 LEU cc_start: 0.8845 (tp) cc_final: 0.8575 (tp) REVERT: A 293 LYS cc_start: 0.8435 (tppt) cc_final: 0.7984 (tppt) REVERT: A 369 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8257 (mtmt) REVERT: A 472 TRP cc_start: 0.9039 (t-100) cc_final: 0.8638 (t-100) REVERT: A 496 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8801 (mt) REVERT: A 537 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8055 (mmmt) REVERT: A 580 LYS cc_start: 0.7198 (tttt) cc_final: 0.6467 (tttm) REVERT: A 681 LYS cc_start: 0.8796 (tppp) cc_final: 0.8430 (tppp) REVERT: A 687 ASP cc_start: 0.8163 (t70) cc_final: 0.7851 (t0) REVERT: A 698 ASP cc_start: 0.7785 (t70) cc_final: 0.7517 (t0) REVERT: A 704 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 712 ASN cc_start: 0.7985 (t0) cc_final: 0.7627 (t0) REVERT: B 66 LYS cc_start: 0.8554 (tptt) cc_final: 0.8237 (tptp) REVERT: B 255 TYR cc_start: 0.8352 (m-10) cc_final: 0.7861 (m-10) REVERT: B 288 LEU cc_start: 0.8884 (tt) cc_final: 0.8466 (mm) REVERT: B 293 LYS cc_start: 0.8571 (tppt) cc_final: 0.8146 (tppt) REVERT: B 320 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 549 ARG cc_start: 0.7730 (ttt180) cc_final: 0.7482 (ttt180) REVERT: B 583 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8246 (tmmt) REVERT: B 698 ASP cc_start: 0.7645 (t70) cc_final: 0.7288 (t0) outliers start: 34 outliers final: 27 residues processed: 254 average time/residue: 0.2903 time to fit residues: 97.2367 Evaluate side-chains 265 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 375 HIS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 696 GLN Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 656 HIS A 730 GLN A 731 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 696 GLN B 705 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10400 Z= 0.225 Angle : 0.696 15.313 14136 Z= 0.348 Chirality : 0.043 0.185 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.018 80.047 1423 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 3.30 % Allowed : 24.87 % Favored : 71.84 % 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: 0.11 (0.24), residues: 1322 helix: 0.91 (0.18), residues: 862 sheet: 0.01 (1.02), residues: 36 loop : -1.62 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 83 HIS 0.015 0.001 HIS B 656 PHE 0.032 0.001 PHE B 210 TYR 0.031 0.001 TYR B 377 ARG 0.010 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8879 (tt) cc_final: 0.8650 (tp) REVERT: A 236 LEU cc_start: 0.8860 (tp) cc_final: 0.8527 (tt) REVERT: A 266 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6896 (p0) REVERT: A 272 PHE cc_start: 0.8490 (t80) cc_final: 0.8023 (t80) REVERT: A 276 LEU cc_start: 0.8993 (mm) cc_final: 0.8362 (mm) REVERT: A 283 MET cc_start: 0.8069 (mmm) cc_final: 0.7817 (mmm) REVERT: A 288 LEU cc_start: 0.8846 (tp) cc_final: 0.8585 (tp) REVERT: A 293 LYS cc_start: 0.8401 (tppt) cc_final: 0.7977 (tppt) REVERT: A 369 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8237 (mtmt) REVERT: A 472 TRP cc_start: 0.9045 (t-100) cc_final: 0.8650 (t-100) REVERT: A 496 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 537 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8035 (mmmt) REVERT: A 580 LYS cc_start: 0.7190 (tttt) cc_final: 0.6604 (tttp) REVERT: A 583 LYS cc_start: 0.8550 (tmtt) cc_final: 0.8304 (tmmt) REVERT: A 687 ASP cc_start: 0.8158 (t70) cc_final: 0.7844 (t0) REVERT: A 698 ASP cc_start: 0.7807 (t70) cc_final: 0.7520 (t0) REVERT: A 704 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 712 ASN cc_start: 0.7985 (t0) cc_final: 0.7712 (t0) REVERT: B 66 LYS cc_start: 0.8558 (tptt) cc_final: 0.8246 (tptp) REVERT: B 255 TYR cc_start: 0.8336 (m-10) cc_final: 0.7762 (m-10) REVERT: B 288 LEU cc_start: 0.8877 (tt) cc_final: 0.8478 (mm) REVERT: B 293 LYS cc_start: 0.8559 (tppt) cc_final: 0.8164 (tppt) REVERT: B 320 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6580 (tm-30) REVERT: B 549 ARG cc_start: 0.7713 (ttt180) cc_final: 0.7484 (ttt180) REVERT: B 583 LYS cc_start: 0.8567 (tmtt) cc_final: 0.8262 (tmmt) REVERT: B 698 ASP cc_start: 0.7648 (t70) cc_final: 0.7283 (t0) outliers start: 37 outliers final: 29 residues processed: 255 average time/residue: 0.2863 time to fit residues: 96.6074 Evaluate side-chains 269 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 HIS Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 706 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 730 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093721 restraints weight = 20832.990| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.03 r_work: 0.3095 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 10400 Z= 0.289 Angle : 0.995 59.192 14136 Z= 0.562 Chirality : 0.059 1.601 1718 Planarity : 0.006 0.165 1758 Dihedral : 5.107 80.065 1423 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 3.48 % Allowed : 24.78 % Favored : 71.75 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.13 (0.24), residues: 1322 helix: 0.92 (0.18), residues: 862 sheet: -0.01 (1.02), residues: 36 loop : -1.61 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 83 HIS 0.252 0.011 HIS B 656 PHE 0.031 0.001 PHE B 210 TYR 0.029 0.001 TYR B 377 ARG 0.009 0.001 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.89 seconds wall clock time: 51 minutes 53.64 seconds (3113.64 seconds total)