Starting phenix.real_space_refine on Fri Feb 14 12:09:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wl8_32577/02_2025/7wl8_32577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wl8_32577/02_2025/7wl8_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/cci-nas-00/data/ceres_data/7wl8_32577/02_2025/7wl8_32577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wl8_32577/02_2025/7wl8_32577.map" model { file = "/net/cci-nas-00/data/ceres_data/7wl8_32577/02_2025/7wl8_32577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wl8_32577/02_2025/7wl8_32577.cif" } 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. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.01, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.4 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: 1.03 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: 2.83 Time building geometry restraints manager: 3.01 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: 0.00 - 1.08: 13606 1.08 - 2.15: 417 2.15 - 3.23: 81 3.23 - 4.30: 19 4.30 - 5.38: 13 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 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.252 3.040 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.265 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.279 3.120 ... (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 Time spend for trying shortcut: 0.05 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.380 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 21 poor density : 335 time to evaluate : 1.092 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: 0.3159 time to fit residues: 141.7443 Evaluate side-chains 277 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 268 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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: 0.3980 chunk 34 optimal weight: 0.0770 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 289 ASN A 421 GLN A 589 GLN A 656 HIS A 696 GLN 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099988 restraints weight = 20828.329| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.96 r_work: 0.3201 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10400 Z= 0.195 Angle : 0.618 8.816 14136 Z= 0.316 Chirality : 0.042 0.163 1718 Planarity : 0.005 0.062 1758 Dihedral : 5.370 80.391 1433 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.32 % Allowed : 16.04 % Favored : 81.64 % 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: -1.87 (0.22), residues: 1322 helix: -0.43 (0.17), residues: 848 sheet: -3.09 (0.66), residues: 48 loop : -2.54 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 518 HIS 0.011 0.001 HIS B 656 PHE 0.019 0.001 PHE A 210 TYR 0.020 0.001 TYR A 377 ARG 0.019 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 302 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7723 (mpp) cc_final: 0.7190 (mpp) REVERT: A 194 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8710 (mm) REVERT: A 213 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8065 (mtt180) REVERT: A 237 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8735 (ttpp) REVERT: A 272 PHE cc_start: 0.8741 (t80) cc_final: 0.8311 (t80) REVERT: A 276 LEU cc_start: 0.9073 (mm) cc_final: 0.8510 (mm) REVERT: A 283 MET cc_start: 0.8644 (mmm) cc_final: 0.8392 (mmm) REVERT: A 318 ASN cc_start: 0.8203 (t0) cc_final: 0.7437 (t0) REVERT: A 384 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8316 (tp30) REVERT: A 463 MET cc_start: 0.8677 (mmm) cc_final: 0.8376 (mmm) REVERT: A 472 TRP cc_start: 0.9134 (t-100) cc_final: 0.8706 (t-100) REVERT: A 488 MET cc_start: 0.8441 (mmm) cc_final: 0.8100 (mmm) REVERT: A 496 LEU cc_start: 0.9254 (mm) cc_final: 0.9009 (mt) REVERT: A 518 TRP cc_start: 0.8784 (p-90) cc_final: 0.8319 (p-90) REVERT: A 537 LYS cc_start: 0.8837 (tppt) cc_final: 0.8282 (tppt) REVERT: A 540 GLU cc_start: 0.8168 (pm20) cc_final: 0.7931 (pm20) REVERT: A 580 LYS cc_start: 0.7432 (tttt) cc_final: 0.6729 (tttm) REVERT: A 582 LEU cc_start: 0.8892 (mt) cc_final: 0.8673 (mp) REVERT: A 681 LYS cc_start: 0.8980 (tppt) cc_final: 0.8717 (tppp) REVERT: A 682 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 685 ARG cc_start: 0.8515 (mtm180) cc_final: 0.7940 (mtm110) REVERT: A 687 ASP cc_start: 0.8820 (t70) cc_final: 0.8418 (t0) REVERT: A 696 GLN cc_start: 0.7347 (mt0) cc_final: 0.6880 (mt0) REVERT: A 698 ASP cc_start: 0.8382 (t70) cc_final: 0.7967 (t0) REVERT: A 701 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8301 (mm-30) REVERT: B 39 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7755 (ttm-80) REVERT: B 66 LYS cc_start: 0.8808 (tptt) cc_final: 0.8346 (tppt) REVERT: B 77 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8430 (ttpp) REVERT: B 161 PHE cc_start: 0.8430 (m-80) cc_final: 0.7901 (m-80) REVERT: B 195 LEU cc_start: 0.8507 (tp) cc_final: 0.8208 (tt) REVERT: B 213 ARG cc_start: 0.8350 (mtt180) cc_final: 0.8020 (mtm180) REVERT: B 277 LEU cc_start: 0.9197 (mm) cc_final: 0.8880 (mm) REVERT: B 287 GLU cc_start: 0.8229 (pp20) cc_final: 0.7903 (pp20) REVERT: B 293 LYS cc_start: 0.8812 (tppt) cc_final: 0.8299 (tppt) REVERT: B 318 ASN cc_start: 0.8280 (t0) cc_final: 0.8017 (t0) REVERT: B 376 ASP cc_start: 0.8060 (t0) cc_final: 0.7482 (t0) REVERT: B 377 TYR cc_start: 0.7019 (p90) cc_final: 0.6800 (p90) REVERT: B 486 CYS cc_start: 0.9170 (t) cc_final: 0.8895 (t) REVERT: B 517 SER cc_start: 0.8360 (p) cc_final: 0.8128 (p) REVERT: B 537 LYS cc_start: 0.8864 (tptt) cc_final: 0.8530 (tptt) REVERT: B 549 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8138 (ttt180) REVERT: B 573 ASP cc_start: 0.7782 (t0) cc_final: 0.7293 (t0) REVERT: B 576 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7500 (mmm160) REVERT: B 579 ASN cc_start: 0.7426 (m110) cc_final: 0.6705 (m-40) REVERT: B 580 LYS cc_start: 0.7908 (tttt) cc_final: 0.7372 (tttm) REVERT: B 583 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8522 (tmtt) REVERT: B 668 LEU cc_start: 0.7210 (mt) cc_final: 0.5799 (tp) REVERT: B 698 ASP cc_start: 0.8410 (t70) cc_final: 0.7958 (t0) REVERT: B 703 MET cc_start: 0.8728 (mtp) cc_final: 0.8472 (mtp) REVERT: B 704 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 705 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7359 (mm-40) REVERT: B 728 HIS cc_start: 0.8712 (t70) cc_final: 0.8308 (t70) outliers start: 26 outliers final: 13 residues processed: 294 average time/residue: 0.2848 time to fit residues: 109.9404 Evaluate side-chains 277 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU 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 A residue 678 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 461 MET 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 51 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 731 ASN ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 728 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095271 restraints weight = 21255.720| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.98 r_work: 0.3118 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10400 Z= 0.253 Angle : 0.617 7.620 14136 Z= 0.319 Chirality : 0.043 0.190 1718 Planarity : 0.004 0.042 1758 Dihedral : 5.369 79.974 1430 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 3.12 % Allowed : 18.63 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1322 helix: 0.23 (0.18), residues: 854 sheet: -1.61 (0.90), residues: 36 loop : -2.33 (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 0.023 0.001 PHE B 210 TYR 0.020 0.001 TYR A 377 ARG 0.008 0.001 ARG B 440 *********************** 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 296 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 PHE cc_start: 0.8636 (p90) cc_final: 0.8402 (p90) REVERT: A 244 THR cc_start: 0.8594 (m) cc_final: 0.8231 (m) REVERT: A 264 ILE cc_start: 0.8974 (mm) cc_final: 0.8757 (mm) REVERT: A 272 PHE cc_start: 0.8862 (t80) cc_final: 0.8400 (t80) REVERT: A 276 LEU cc_start: 0.9141 (mm) cc_final: 0.8534 (mm) REVERT: A 283 MET cc_start: 0.8779 (mmm) cc_final: 0.8489 (mmm) REVERT: A 293 LYS cc_start: 0.8627 (tppt) cc_final: 0.8119 (tppt) REVERT: A 318 ASN cc_start: 0.8478 (t0) cc_final: 0.8028 (t0) REVERT: A 463 MET cc_start: 0.8741 (mmm) cc_final: 0.8482 (mmm) REVERT: A 472 TRP cc_start: 0.9226 (t-100) cc_final: 0.8912 (t-100) REVERT: A 473 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8740 (mmmm) REVERT: A 488 MET cc_start: 0.8464 (mmm) cc_final: 0.8256 (mmm) REVERT: A 499 LEU cc_start: 0.8792 (mm) cc_final: 0.8577 (tp) REVERT: A 537 LYS cc_start: 0.8893 (tppt) cc_final: 0.8380 (mmtt) REVERT: A 541 GLU cc_start: 0.8292 (mp0) cc_final: 0.8066 (mp0) REVERT: A 580 LYS cc_start: 0.7469 (tttt) cc_final: 0.6783 (tttm) REVERT: A 682 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 687 ASP cc_start: 0.8813 (t70) cc_final: 0.8444 (t0) REVERT: A 696 GLN cc_start: 0.7568 (mt0) cc_final: 0.7286 (mt0) REVERT: A 698 ASP cc_start: 0.8508 (t70) cc_final: 0.8136 (t0) REVERT: B 38 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7988 (mtp-110) REVERT: B 39 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7763 (mtp85) REVERT: B 66 LYS cc_start: 0.8819 (tptt) cc_final: 0.8315 (tppt) REVERT: B 77 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8493 (ttpp) REVERT: B 195 LEU cc_start: 0.8515 (tp) cc_final: 0.8287 (tt) REVERT: B 213 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8078 (mtm180) REVERT: B 259 GLU cc_start: 0.8869 (tt0) cc_final: 0.8422 (tm-30) REVERT: B 277 LEU cc_start: 0.9226 (mm) cc_final: 0.9002 (mm) REVERT: B 293 LYS cc_start: 0.8798 (tppt) cc_final: 0.8230 (tppt) REVERT: B 318 ASN cc_start: 0.8445 (t0) cc_final: 0.7942 (t0) REVERT: B 320 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 324 ASN cc_start: 0.9086 (t0) cc_final: 0.8657 (t0) REVERT: B 376 ASP cc_start: 0.7872 (t0) cc_final: 0.7633 (t0) REVERT: B 384 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8163 (mm-30) REVERT: B 443 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 466 CYS cc_start: 0.8732 (m) cc_final: 0.8475 (p) REVERT: B 486 CYS cc_start: 0.9142 (t) cc_final: 0.8882 (t) REVERT: B 517 SER cc_start: 0.8561 (p) cc_final: 0.8336 (p) REVERT: B 537 LYS cc_start: 0.8975 (tptt) cc_final: 0.8628 (tptt) REVERT: B 549 ARG cc_start: 0.8727 (ttt180) cc_final: 0.8359 (ttt180) REVERT: B 583 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8559 (tmtt) REVERT: B 669 ASP cc_start: 0.7501 (t0) cc_final: 0.7069 (t70) REVERT: B 698 ASP cc_start: 0.8445 (t70) cc_final: 0.7975 (t0) REVERT: B 704 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 732 GLN cc_start: 0.7543 (tp-100) cc_final: 0.7104 (tp40) outliers start: 35 outliers final: 24 residues processed: 278 average time/residue: 0.2872 time to fit residues: 105.0361 Evaluate side-chains 271 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 308 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 79 ARG 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 496 LEU 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 585 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 118 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 712 ASN ** B 375 HIS ** 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 = 0.3574 r_free = 0.3574 target = 0.111863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094936 restraints weight = 20876.972| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.95 r_work: 0.3113 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10400 Z= 0.227 Angle : 0.609 8.338 14136 Z= 0.313 Chirality : 0.043 0.177 1718 Planarity : 0.004 0.041 1758 Dihedral : 5.395 81.088 1430 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 3.65 % Allowed : 19.52 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.24), residues: 1322 helix: 0.47 (0.18), residues: 858 sheet: -0.89 (0.97), residues: 34 loop : -2.12 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 83 HIS 0.012 0.001 HIS B 656 PHE 0.025 0.001 PHE B 210 TYR 0.019 0.001 TYR A 377 ARG 0.006 0.000 ARG A 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 304 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ILE cc_start: 0.8975 (mm) cc_final: 0.8734 (mm) REVERT: A 272 PHE cc_start: 0.8901 (t80) cc_final: 0.8397 (t80) REVERT: A 276 LEU cc_start: 0.9178 (mm) cc_final: 0.8554 (mm) REVERT: A 283 MET cc_start: 0.8789 (mmm) cc_final: 0.8452 (mmm) REVERT: A 293 LYS cc_start: 0.8596 (tppt) cc_final: 0.8089 (tppt) REVERT: A 318 ASN cc_start: 0.8412 (t0) cc_final: 0.8071 (t0) REVERT: A 374 LYS cc_start: 0.8561 (tmmt) cc_final: 0.8109 (ttpp) REVERT: A 463 MET cc_start: 0.8745 (mmm) cc_final: 0.8448 (mmm) REVERT: A 472 TRP cc_start: 0.9184 (t-100) cc_final: 0.8976 (t-100) REVERT: A 488 MET cc_start: 0.8466 (mmm) cc_final: 0.8240 (mmm) REVERT: A 537 LYS cc_start: 0.8911 (tppt) cc_final: 0.8399 (mmtt) REVERT: A 541 GLU cc_start: 0.8314 (mp0) cc_final: 0.8081 (mp0) REVERT: A 549 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8166 (ttm-80) REVERT: A 580 LYS cc_start: 0.7414 (tttt) cc_final: 0.6770 (tttp) REVERT: A 682 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 687 ASP cc_start: 0.8819 (t70) cc_final: 0.8451 (t0) REVERT: A 696 GLN cc_start: 0.7598 (mt0) cc_final: 0.7113 (mt0) REVERT: A 698 ASP cc_start: 0.8472 (t70) cc_final: 0.8091 (t0) REVERT: A 712 ASN cc_start: 0.8586 (t0) cc_final: 0.8251 (t0) REVERT: B 39 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7789 (mtp85) REVERT: B 66 LYS cc_start: 0.8808 (tptt) cc_final: 0.8291 (tppt) REVERT: B 77 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8360 (ttpp) REVERT: B 195 LEU cc_start: 0.8515 (tp) cc_final: 0.8269 (tt) REVERT: B 213 ARG cc_start: 0.8416 (mtt180) cc_final: 0.8178 (mtm-85) REVERT: B 245 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7646 (ttpp) REVERT: B 259 GLU cc_start: 0.8828 (tt0) cc_final: 0.8380 (tm-30) REVERT: B 288 LEU cc_start: 0.8678 (tt) cc_final: 0.8244 (mm) REVERT: B 293 LYS cc_start: 0.8810 (tppt) cc_final: 0.8234 (tppt) REVERT: B 318 ASN cc_start: 0.8465 (t0) cc_final: 0.8134 (t0) REVERT: B 320 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 324 ASN cc_start: 0.9064 (t0) cc_final: 0.8638 (t0) REVERT: B 376 ASP cc_start: 0.7958 (t0) cc_final: 0.7742 (t0) REVERT: B 384 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 443 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 466 CYS cc_start: 0.8723 (m) cc_final: 0.8464 (p) REVERT: B 486 CYS cc_start: 0.9119 (t) cc_final: 0.8852 (t) REVERT: B 517 SER cc_start: 0.8382 (p) cc_final: 0.8116 (p) REVERT: B 537 LYS cc_start: 0.8957 (tptt) cc_final: 0.8601 (tptt) REVERT: B 549 ARG cc_start: 0.8695 (ttt180) cc_final: 0.8248 (ttt180) REVERT: B 583 LYS cc_start: 0.8937 (tmtt) cc_final: 0.8612 (tmtt) REVERT: B 587 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7240 (mmm-85) REVERT: B 669 ASP cc_start: 0.7499 (t0) cc_final: 0.7101 (t0) REVERT: B 696 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7003 (mm-40) REVERT: B 698 ASP cc_start: 0.8424 (t70) cc_final: 0.7953 (t0) REVERT: B 704 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8271 (tm-30) outliers start: 41 outliers final: 29 residues processed: 284 average time/residue: 0.2851 time to fit residues: 106.6441 Evaluate side-chains 282 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 345 LEU 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 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 79 ARG 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 242 VAL 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 529 ILE Chi-restraints excluded: chain B residue 543 GLU 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 706 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 31 optimal weight: 0.0060 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 131 optimal weight: 0.9980 overall best weight: 0.1954 ------------------------------------------------------------------------------- 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 B 375 HIS B 656 HIS ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096947 restraints weight = 20842.194| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.98 r_work: 0.3154 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3659 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= 0.175 Angle : 0.591 7.452 14136 Z= 0.303 Chirality : 0.042 0.177 1718 Planarity : 0.004 0.052 1758 Dihedral : 5.373 81.828 1428 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.21 % Allowed : 22.01 % Favored : 74.78 % 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: -0.34 (0.24), residues: 1322 helix: 0.63 (0.18), residues: 860 sheet: -0.72 (0.96), residues: 34 loop : -1.90 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 83 HIS 0.014 0.001 HIS B 656 PHE 0.025 0.001 PHE B 210 TYR 0.032 0.001 TYR B 377 ARG 0.012 0.000 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 296 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 1.158 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: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8952 (tp) cc_final: 0.8683 (tt) REVERT: A 272 PHE cc_start: 0.8885 (t80) cc_final: 0.8370 (t80) REVERT: A 276 LEU cc_start: 0.9161 (mm) cc_final: 0.8524 (mm) REVERT: A 283 MET cc_start: 0.8774 (mmm) cc_final: 0.8418 (mmm) REVERT: A 293 LYS cc_start: 0.8573 (tppt) cc_final: 0.8061 (tppt) REVERT: A 318 ASN cc_start: 0.8359 (t0) cc_final: 0.8002 (t0) REVERT: A 374 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8302 (ttpp) REVERT: A 414 GLU cc_start: 0.7820 (tp30) cc_final: 0.7550 (tp30) REVERT: A 426 ILE cc_start: 0.8783 (tp) cc_final: 0.8572 (tp) REVERT: A 463 MET cc_start: 0.8778 (mmm) cc_final: 0.8451 (mmm) REVERT: A 472 TRP cc_start: 0.9112 (t-100) cc_final: 0.8593 (t-100) REVERT: A 473 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8677 (tppp) REVERT: A 488 MET cc_start: 0.8410 (mmm) cc_final: 0.8181 (mmm) REVERT: A 537 LYS cc_start: 0.8866 (tppt) cc_final: 0.8377 (mmtt) REVERT: A 541 GLU cc_start: 0.8399 (mp0) cc_final: 0.8153 (mp0) REVERT: A 580 LYS cc_start: 0.7405 (tttt) cc_final: 0.6591 (tttp) REVERT: A 681 LYS cc_start: 0.9048 (tppp) cc_final: 0.8659 (tppp) REVERT: A 682 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 685 ARG cc_start: 0.8667 (mtm110) cc_final: 0.8227 (ttp-110) REVERT: A 687 ASP cc_start: 0.8766 (t70) cc_final: 0.8422 (t0) REVERT: A 696 GLN cc_start: 0.7548 (mt0) cc_final: 0.7084 (mt0) REVERT: A 698 ASP cc_start: 0.8464 (t70) cc_final: 0.8081 (t0) REVERT: A 704 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 712 ASN cc_start: 0.8590 (t0) cc_final: 0.8169 (t0) REVERT: B 66 LYS cc_start: 0.8788 (tptt) cc_final: 0.8210 (tppt) REVERT: B 77 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8288 (ttpp) REVERT: B 195 LEU cc_start: 0.8511 (tp) cc_final: 0.8282 (tt) REVERT: B 213 ARG cc_start: 0.8358 (mtt180) cc_final: 0.8122 (mtm-85) REVERT: B 259 GLU cc_start: 0.8735 (tt0) cc_final: 0.8205 (tm-30) REVERT: B 277 LEU cc_start: 0.9224 (mm) cc_final: 0.9013 (mm) REVERT: B 288 LEU cc_start: 0.8650 (tt) cc_final: 0.8230 (mm) REVERT: B 293 LYS cc_start: 0.8793 (tppt) cc_final: 0.8221 (tppt) REVERT: B 318 ASN cc_start: 0.8461 (t0) cc_final: 0.8147 (t0) REVERT: B 320 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 324 ASN cc_start: 0.9055 (t0) cc_final: 0.8626 (t0) REVERT: B 369 LYS cc_start: 0.8841 (mttp) cc_final: 0.8561 (ttmt) REVERT: B 374 LYS cc_start: 0.8666 (tmtt) cc_final: 0.8355 (ttpp) REVERT: B 384 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8191 (mm-30) REVERT: B 443 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8029 (tm-30) REVERT: B 486 CYS cc_start: 0.9135 (t) cc_final: 0.8871 (t) REVERT: B 517 SER cc_start: 0.8308 (p) cc_final: 0.8041 (p) REVERT: B 537 LYS cc_start: 0.8958 (tptt) cc_final: 0.8585 (tptt) REVERT: B 549 ARG cc_start: 0.8700 (ttt180) cc_final: 0.8261 (ttt180) REVERT: B 583 LYS cc_start: 0.8929 (tmtt) cc_final: 0.8584 (tmtt) REVERT: B 587 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7073 (mmm-85) REVERT: B 652 LYS cc_start: 0.7404 (pttt) cc_final: 0.7197 (pttt) REVERT: B 698 ASP cc_start: 0.8403 (t70) cc_final: 0.7943 (t0) REVERT: B 704 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8308 (tm-30) outliers start: 36 outliers final: 23 residues processed: 280 average time/residue: 0.2802 time to fit residues: 103.3283 Evaluate side-chains 276 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 492 LEU 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 79 ARG 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 242 VAL 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 543 GLU Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5774 > 50: distance: 29 - 31: 11.089 distance: 31 - 32: 12.795 distance: 32 - 33: 17.225 distance: 32 - 35: 10.567 distance: 33 - 34: 10.811 distance: 33 - 39: 5.017 distance: 35 - 36: 15.875 distance: 36 - 37: 11.191 distance: 36 - 38: 10.064 distance: 39 - 40: 15.140 distance: 40 - 41: 15.331 distance: 41 - 42: 17.007 distance: 41 - 43: 19.949 distance: 43 - 44: 11.751 distance: 44 - 45: 17.901 distance: 44 - 47: 20.764 distance: 45 - 46: 8.159 distance: 45 - 49: 30.325 distance: 47 - 48: 20.253 distance: 49 - 50: 11.737 distance: 50 - 51: 22.675 distance: 50 - 53: 13.025 distance: 51 - 52: 16.488 distance: 51 - 54: 16.965 distance: 54 - 55: 17.516 distance: 55 - 56: 12.626 distance: 55 - 58: 15.290 distance: 56 - 57: 21.451 distance: 56 - 62: 21.526 distance: 58 - 59: 15.935 distance: 59 - 60: 10.682 distance: 59 - 61: 22.182 distance: 62 - 63: 40.609 distance: 63 - 64: 25.719 distance: 63 - 66: 17.090 distance: 64 - 65: 24.042 distance: 64 - 70: 14.243 distance: 66 - 67: 40.018 distance: 67 - 68: 5.337 distance: 67 - 69: 45.160 distance: 70 - 71: 15.899 distance: 71 - 72: 9.998 distance: 71 - 74: 26.890 distance: 72 - 73: 33.883 distance: 72 - 76: 31.125 distance: 74 - 75: 43.466 distance: 76 - 77: 13.502 distance: 77 - 78: 9.449 distance: 77 - 80: 13.229 distance: 78 - 79: 29.494 distance: 78 - 83: 11.275 distance: 80 - 81: 25.421 distance: 80 - 82: 40.910 distance: 83 - 84: 19.269 distance: 84 - 85: 21.297 distance: 84 - 87: 25.169 distance: 85 - 86: 20.193 distance: 85 - 90: 4.671 distance: 87 - 88: 20.803 distance: 87 - 89: 19.740 distance: 90 - 91: 12.874 distance: 91 - 92: 19.195 distance: 91 - 94: 20.775 distance: 92 - 93: 38.523 distance: 92 - 98: 28.267 distance: 94 - 95: 29.436 distance: 95 - 96: 12.131 distance: 95 - 97: 19.276