Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 17 20:24:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/08_2023/8ffk_29045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/08_2023/8ffk_29045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/08_2023/8ffk_29045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/08_2023/8ffk_29045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/08_2023/8ffk_29045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffk_29045/08_2023/8ffk_29045.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.051 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 131 5.16 5 C 15120 2.51 5 N 3873 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 23482 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7819 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 985} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7840 Classifications: {'peptide': 1033} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 985} Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7823 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 985} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 11.64, per 1000 atoms: 0.50 Number of scatterers: 23482 At special positions: 0 Unit cell: (112.35, 121.98, 145.52, 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 131 16.00 O 4358 8.00 N 3873 7.00 C 15120 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: 10.96 Conformation dependent library (CDL) restraints added in 3.7 seconds 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 24 sheets defined 60.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.859A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.509A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 298 through 313 Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 370 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 401 through 423 Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.279A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 460 through 497 removed outlier: 4.752A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.610A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 536 removed outlier: 3.709A pdb=" N GLY A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.395A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 638 through 641 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.574A pdb=" N GLN A 707 " --> pdb=" O GLY A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 781 through 787 Processing helix chain 'A' and resid 800 through 803 No H-bonds generated for 'chain 'A' and resid 800 through 803' Processing helix chain 'A' and resid 835 through 849 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.594A pdb=" N GLN A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 892 removed outlier: 3.623A pdb=" N ALA A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 902 removed outlier: 3.864A pdb=" N VAL A 900 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 918 removed outlier: 3.618A pdb=" N GLY A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 955 Processing helix chain 'A' and resid 958 through 991 removed outlier: 4.726A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Proline residue: A 973 - end of helix Proline residue: A 987 - end of helix Processing helix chain 'A' and resid 995 through 1032 removed outlier: 4.163A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Proline residue: A1022 - end of helix Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.703A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.933A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.554A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 386 removed outlier: 3.695A pdb=" N VAL B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.219A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.776A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.519A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 536 Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.963A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 638 through 641 Processing helix chain 'B' and resid 642 through 655 Processing helix chain 'B' and resid 690 through 707 Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 741 through 754 Processing helix chain 'B' and resid 781 through 787 removed outlier: 3.689A pdb=" N GLY B 786 " --> pdb=" O GLU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 803 No H-bonds generated for 'chain 'B' and resid 800 through 803' Processing helix chain 'B' and resid 835 through 849 Processing helix chain 'B' and resid 860 through 892 removed outlier: 3.501A pdb=" N GLN B 864 " --> pdb=" O GLY B 860 " (cutoff:3.500A) Proline residue: B 873 - end of helix Processing helix chain 'B' and resid 894 through 902 removed outlier: 3.506A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 918 removed outlier: 3.630A pdb=" N GLY B 907 " --> pdb=" O VAL B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 956 removed outlier: 4.256A pdb=" N PHE B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 970 Processing helix chain 'B' and resid 970 through 991 Proline residue: B 987 - end of helix Processing helix chain 'B' and resid 995 through 1016 removed outlier: 4.581A pdb=" N GLY B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1032 Proline residue: B1022 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 4.068A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.960A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.618A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.500A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 454 removed outlier: 5.258A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.648A pdb=" N PHE C 459 " --> pdb=" O MET C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 497 removed outlier: 3.618A pdb=" N TYR C 467 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 510 through 537 Processing helix chain 'C' and resid 538 through 558 Processing helix chain 'C' and resid 582 through 600 Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 638 through 641 Processing helix chain 'C' and resid 642 through 658 Processing helix chain 'C' and resid 690 through 707 Processing helix chain 'C' and resid 731 through 739 Processing helix chain 'C' and resid 741 through 755 Processing helix chain 'C' and resid 776 through 779 Processing helix chain 'C' and resid 781 through 787 removed outlier: 3.524A pdb=" N GLY C 786 " --> pdb=" O GLU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 848 Processing helix chain 'C' and resid 860 through 868 Processing helix chain 'C' and resid 871 through 892 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.001A pdb=" N VAL C 900 " --> pdb=" O ILE C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 919 removed outlier: 3.944A pdb=" N GLY C 907 " --> pdb=" O VAL C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 955 Processing helix chain 'C' and resid 958 through 990 removed outlier: 4.726A pdb=" N ARG C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Proline residue: C 973 - end of helix Proline residue: C 987 - end of helix Processing helix chain 'C' and resid 995 through 1032 removed outlier: 4.084A pdb=" N PHE C1019 " --> pdb=" O ILE C1015 " (cutoff:3.500A) Proline residue: C1022 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.926A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 12.452A pdb=" N ARG A 814 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 825 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 816 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.926A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 12.452A pdb=" N ARG A 814 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 825 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 816 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU A 825 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 827 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 715 " --> pdb=" O LEU A 827 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.054A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.054A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.743A pdb=" N TYR A 182 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS A 769 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 759 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 772 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR A 757 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.380A pdb=" N ILE A 235 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 730 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA8, first strand: chain 'A' and resid 804 through 811 removed outlier: 8.472A pdb=" N ILE C 235 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 726 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 789 through 791 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.018A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.013A pdb=" N ARG B 814 " --> pdb=" O GLU B 825 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU B 825 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 816 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN B 829 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY B 714 " --> pdb=" O GLN B 829 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.018A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.013A pdb=" N ARG B 814 " --> pdb=" O GLU B 825 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU B 825 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 816 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 828 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.558A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.558A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER B 629 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 610 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 625 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.374A pdb=" N TYR B 182 " --> pdb=" O VAL B 767 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 769 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN B 759 " --> pdb=" O VAL B 770 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE B 772 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR B 757 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.707A pdb=" N SER B 233 " --> pdb=" O PRO C 724 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.937A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 789 through 791 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.157A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.366A pdb=" N ARG C 814 " --> pdb=" O GLU C 825 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLU C 825 " --> pdb=" O ARG C 814 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU C 816 " --> pdb=" O SER C 823 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 825 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN C 829 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY C 714 " --> pdb=" O GLN C 829 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.157A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.366A pdb=" N ARG C 814 " --> pdb=" O GLU C 825 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLU C 825 " --> pdb=" O ARG C 814 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU C 816 " --> pdb=" O SER C 823 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP C 680 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.946A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.258A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 629 " --> pdb=" O GLU C 606 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 608 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE C 627 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA C 610 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 625 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASN C 612 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR C 623 " --> pdb=" O ASN C 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.457A pdb=" N TYR C 182 " --> pdb=" O VAL C 767 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 769 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN C 759 " --> pdb=" O VAL C 770 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE C 772 " --> pdb=" O TYR C 757 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TYR C 757 " --> pdb=" O ILE C 772 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 253 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 791 1687 hydrogen bonds defined for protein. 4890 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: 10.85 Time building geometry restraints manager: 11.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7563 1.34 - 1.45: 3091 1.45 - 1.57: 13036 1.57 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 23946 Sorted by residual: bond pdb=" CA ASP B 923 " pdb=" C ASP B 923 " ideal model delta sigma weight residual 1.530 1.505 0.026 1.12e-02 7.97e+03 5.29e+00 bond pdb=" CA TYR C 182 " pdb=" C TYR C 182 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.30e-02 5.92e+03 3.96e+00 bond pdb=" C ARG A 972 " pdb=" O ARG A 972 " ideal model delta sigma weight residual 1.244 1.225 0.019 1.00e-02 1.00e+04 3.48e+00 bond pdb=" CA ARG A 968 " pdb=" C ARG A 968 " ideal model delta sigma weight residual 1.524 1.502 0.021 1.27e-02 6.20e+03 2.85e+00 bond pdb=" CA SER B 561 " pdb=" CB SER B 561 " ideal model delta sigma weight residual 1.538 1.518 0.020 1.22e-02 6.72e+03 2.62e+00 ... (remaining 23941 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.26: 694 106.26 - 113.19: 13129 113.19 - 120.13: 8057 120.13 - 127.06: 10433 127.06 - 133.99: 219 Bond angle restraints: 32532 Sorted by residual: angle pdb=" C GLY B 221 " pdb=" N THR B 222 " pdb=" CA THR B 222 " ideal model delta sigma weight residual 120.49 127.05 -6.56 1.42e+00 4.96e-01 2.13e+01 angle pdb=" C ARG A 972 " pdb=" N PRO A 973 " pdb=" CA PRO A 973 " ideal model delta sigma weight residual 119.05 114.65 4.40 1.11e+00 8.12e-01 1.57e+01 angle pdb=" C THR B 60 " pdb=" N VAL B 61 " pdb=" CA VAL B 61 " ideal model delta sigma weight residual 123.16 118.98 4.18 1.06e+00 8.90e-01 1.55e+01 angle pdb=" N ARG A 968 " pdb=" CA ARG A 968 " pdb=" C ARG A 968 " ideal model delta sigma weight residual 111.07 107.03 4.04 1.07e+00 8.73e-01 1.43e+01 angle pdb=" N GLY A 531 " pdb=" CA GLY A 531 " pdb=" C GLY A 531 " ideal model delta sigma weight residual 112.50 108.55 3.95 1.16e+00 7.43e-01 1.16e+01 ... (remaining 32527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 13429 17.16 - 34.33: 672 34.33 - 51.49: 134 51.49 - 68.65: 14 68.65 - 85.81: 5 Dihedral angle restraints: 14254 sinusoidal: 5446 harmonic: 8808 Sorted by residual: dihedral pdb=" CA SER C 536 " pdb=" C SER C 536 " pdb=" N THR C 537 " pdb=" CA THR C 537 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA A 706 " pdb=" C ALA A 706 " pdb=" N GLN A 707 " pdb=" CA GLN A 707 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA SER A 774 " pdb=" C SER A 774 " pdb=" N GLU A 775 " pdb=" CA GLU A 775 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 ... (remaining 14251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2633 0.036 - 0.071: 832 0.071 - 0.107: 259 0.107 - 0.142: 84 0.142 - 0.177: 3 Chirality restraints: 3811 Sorted by residual: chirality pdb=" CB ILE C 367 " pdb=" CA ILE C 367 " pdb=" CG1 ILE C 367 " pdb=" CG2 ILE C 367 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL C1021 " pdb=" CA VAL C1021 " pdb=" CG1 VAL C1021 " pdb=" CG2 VAL C1021 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 3808 not shown) Planarity restraints: 4170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 965 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C GLU A 965 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 965 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA A 966 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 199 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 200 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 498 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 499 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.021 5.00e-02 4.00e+02 ... (remaining 4167 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1982 2.74 - 3.28: 24286 3.28 - 3.82: 40750 3.82 - 4.36: 48707 4.36 - 4.90: 85600 Nonbonded interactions: 201325 Sorted by model distance: nonbonded pdb=" OH TYR B 467 " pdb=" OE1 GLN B 927 " model vdw 2.195 2.440 nonbonded pdb=" O ILE A 974 " pdb=" OG SER A 978 " model vdw 2.200 2.440 nonbonded pdb=" O LYS C 631 " pdb=" NH1 ARG C 636 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR A 757 " pdb=" OD1 ASP A 760 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR A 467 " pdb=" OE1 GLN A 927 " model vdw 2.213 2.440 ... (remaining 201320 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' and (resid 2 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or resid 503 through 1030 or (resid 1031 \ and (name N or name CA or name C or name O or name CB )) or resid 1032 through 1 \ 033)) selection = (chain 'B' and (resid 2 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or resid 503 through 504 or (resid 505 an \ d (name N or name CA or name C or name O or name CB )) or resid 506 through 671 \ or (resid 672 and (name N or name CA or name C or name O or name CB )) or resid \ 673 through 1030 or (resid 1031 and (name N or name CA or name C or name O or na \ me CB )) or resid 1032 through 1033)) selection = (chain 'C' and (resid 2 through 504 or (resid 505 and (name N or name CA or name \ C or name O or name CB )) or resid 506 through 671 or (resid 672 and (name N or \ name CA or name C or name O or name CB )) or resid 673 through 1033)) } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.270 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 66.500 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.004 0.040 23946 Z= 0.274 Angle : 0.556 8.642 32532 Z= 0.311 Chirality : 0.041 0.177 3811 Planarity : 0.004 0.040 4170 Dihedral : 10.749 85.814 8622 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.77 (0.15), residues: 3092 helix: 2.20 (0.12), residues: 1704 sheet: -0.19 (0.25), residues: 411 loop : 0.01 (0.20), residues: 977 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 475 time to evaluate : 2.620 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 21 residues processed: 516 average time/residue: 1.3569 time to fit residues: 801.7733 Evaluate side-chains 324 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 303 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.2557 time to fit residues: 4.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 210 GLN A 415 ASN A 656 GLN B 104 GLN B 108 GLN B 109 ASN B 144 ASN B 360 GLN B 516 ASN B 583 GLN B 700 GLN B 708 HIS B 718 ASN C 58 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 415 ASN C 576 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN C 686 GLN C 736 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 23946 Z= 0.216 Angle : 0.537 8.189 32532 Z= 0.281 Chirality : 0.042 0.186 3811 Planarity : 0.004 0.035 4170 Dihedral : 4.010 18.826 3283 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.92 (0.15), residues: 3092 helix: 2.36 (0.12), residues: 1723 sheet: -0.20 (0.25), residues: 406 loop : 0.00 (0.20), residues: 963 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 340 time to evaluate : 2.893 Fit side-chains revert: symmetry clash outliers start: 96 outliers final: 36 residues processed: 402 average time/residue: 1.3049 time to fit residues: 609.6432 Evaluate side-chains 330 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 294 time to evaluate : 2.577 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 30 residues processed: 8 average time/residue: 0.8998 time to fit residues: 12.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 281 optimal weight: 0.0670 chunk 303 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A1000 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 23946 Z= 0.226 Angle : 0.523 8.328 32532 Z= 0.272 Chirality : 0.042 0.173 3811 Planarity : 0.004 0.044 4170 Dihedral : 4.008 18.106 3283 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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 (0.15), residues: 3092 helix: 2.33 (0.12), residues: 1729 sheet: -0.18 (0.25), residues: 395 loop : -0.08 (0.20), residues: 968 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 319 time to evaluate : 2.862 Fit side-chains revert: symmetry clash outliers start: 94 outliers final: 43 residues processed: 377 average time/residue: 1.2692 time to fit residues: 556.5102 Evaluate side-chains 337 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 294 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 32 residues processed: 13 average time/residue: 0.5222 time to fit residues: 12.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 145 optimal weight: 0.0030 chunk 31 optimal weight: 4.9990 chunk 134 optimal weight: 0.0040 chunk 188 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN B 718 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23946 Z= 0.202 Angle : 0.513 8.513 32532 Z= 0.266 Chirality : 0.041 0.168 3811 Planarity : 0.004 0.047 4170 Dihedral : 3.969 18.104 3283 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.89 (0.15), residues: 3092 helix: 2.37 (0.12), residues: 1729 sheet: -0.19 (0.25), residues: 398 loop : -0.12 (0.20), residues: 965 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 318 time to evaluate : 2.666 Fit side-chains revert: symmetry clash outliers start: 97 outliers final: 46 residues processed: 386 average time/residue: 1.1938 time to fit residues: 539.4050 Evaluate side-chains 349 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 303 time to evaluate : 2.705 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 40 residues processed: 8 average time/residue: 0.5378 time to fit residues: 9.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 254 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 0.0170 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 439 GLN B 195 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 23946 Z= 0.247 Angle : 0.530 9.264 32532 Z= 0.273 Chirality : 0.042 0.174 3811 Planarity : 0.004 0.049 4170 Dihedral : 3.997 17.993 3283 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.83 (0.15), residues: 3092 helix: 2.31 (0.12), residues: 1732 sheet: -0.14 (0.25), residues: 393 loop : -0.17 (0.20), residues: 967 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 312 time to evaluate : 2.492 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 57 residues processed: 373 average time/residue: 1.2547 time to fit residues: 547.0220 Evaluate side-chains 356 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 299 time to evaluate : 2.895 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 45 residues processed: 14 average time/residue: 0.5507 time to fit residues: 14.1173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23946 Z= 0.191 Angle : 0.510 9.203 32532 Z= 0.263 Chirality : 0.041 0.166 3811 Planarity : 0.004 0.049 4170 Dihedral : 3.942 18.083 3283 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.88 (0.15), residues: 3092 helix: 2.36 (0.12), residues: 1730 sheet: -0.17 (0.25), residues: 410 loop : -0.12 (0.20), residues: 952 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 317 time to evaluate : 2.610 Fit side-chains revert: symmetry clash outliers start: 78 outliers final: 50 residues processed: 376 average time/residue: 1.2404 time to fit residues: 552.4784 Evaluate side-chains 352 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 302 time to evaluate : 2.720 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 44 residues processed: 8 average time/residue: 0.5745 time to fit residues: 10.0833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 170 optimal weight: 0.0770 chunk 218 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 439 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 23946 Z= 0.215 Angle : 0.524 9.233 32532 Z= 0.269 Chirality : 0.041 0.168 3811 Planarity : 0.004 0.050 4170 Dihedral : 3.952 17.910 3283 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.86 (0.15), residues: 3092 helix: 2.32 (0.12), residues: 1730 sheet: -0.12 (0.25), residues: 407 loop : -0.14 (0.20), residues: 955 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 307 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 53 residues processed: 369 average time/residue: 1.2332 time to fit residues: 535.1608 Evaluate side-chains 349 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 296 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 47 residues processed: 8 average time/residue: 0.7415 time to fit residues: 11.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 0.3980 chunk 147 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 23946 Z= 0.173 Angle : 0.506 7.946 32532 Z= 0.260 Chirality : 0.040 0.162 3811 Planarity : 0.004 0.050 4170 Dihedral : 3.885 18.294 3283 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.89 (0.15), residues: 3092 helix: 2.34 (0.12), residues: 1728 sheet: -0.18 (0.24), residues: 432 loop : -0.05 (0.21), residues: 932 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 326 time to evaluate : 2.799 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 50 residues processed: 380 average time/residue: 1.2168 time to fit residues: 543.4680 Evaluate side-chains 353 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 303 time to evaluate : 2.561 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 45 residues processed: 7 average time/residue: 0.6039 time to fit residues: 9.2499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 2.9990 chunk 285 optimal weight: 0.4980 chunk 260 optimal weight: 0.9980 chunk 277 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 217 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 276 optimal weight: 0.1980 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 439 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 23946 Z= 0.173 Angle : 0.517 8.345 32532 Z= 0.265 Chirality : 0.041 0.226 3811 Planarity : 0.004 0.051 4170 Dihedral : 3.844 18.341 3283 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 3092 helix: 2.35 (0.12), residues: 1728 sheet: -0.16 (0.24), residues: 442 loop : -0.06 (0.21), residues: 922 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 312 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 47 residues processed: 360 average time/residue: 1.2284 time to fit residues: 517.7652 Evaluate side-chains 349 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 302 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 45 residues processed: 3 average time/residue: 1.2761 time to fit residues: 8.6717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 283 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 23946 Z= 0.196 Angle : 0.527 8.219 32532 Z= 0.270 Chirality : 0.041 0.206 3811 Planarity : 0.004 0.051 4170 Dihedral : 3.870 19.181 3283 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 3092 helix: 2.33 (0.12), residues: 1729 sheet: -0.12 (0.24), residues: 429 loop : -0.05 (0.21), residues: 934 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 307 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 48 residues processed: 356 average time/residue: 1.2661 time to fit residues: 528.2352 Evaluate side-chains 350 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 302 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 45 residues processed: 4 average time/residue: 0.9933 time to fit residues: 8.2058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN B 68 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** 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 = 0.3443 r_free = 0.3443 target = 0.116757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099509 restraints weight = 32269.515| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.81 r_work: 0.3079 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 23946 Z= 0.199 Angle : 0.531 8.234 32532 Z= 0.271 Chirality : 0.041 0.207 3811 Planarity : 0.004 0.049 4170 Dihedral : 3.867 18.570 3283 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % 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: 1.89 (0.15), residues: 3092 helix: 2.32 (0.12), residues: 1729 sheet: -0.10 (0.24), residues: 429 loop : -0.04 (0.21), residues: 934 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8764.51 seconds wall clock time: 156 minutes 16.69 seconds (9376.69 seconds total)