Starting phenix.real_space_refine on Wed May 15 05:02:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/05_2024/8wfn_37497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/05_2024/8wfn_37497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/05_2024/8wfn_37497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/05_2024/8wfn_37497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/05_2024/8wfn_37497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfn_37497/05_2024/8wfn_37497.pdb" } resolution = 4.48 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= 0.094 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 111 5.16 5 C 19101 2.51 5 N 4763 2.21 5 O 5557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 29532 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 8016 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 944} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 8117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 8117 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 956} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 851 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5585 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 652} Chain breaks: 13 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5492 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 646} Chain breaks: 14 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 312 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain breaks: 5 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain breaks: 4 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 15.35, per 1000 atoms: 0.52 Number of scatterers: 29532 At special positions: 0 Unit cell: (105.4, 132.6, 243.1, 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 111 16.00 O 5557 8.00 N 4763 7.00 C 19101 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: 11.82 Conformation dependent library (CDL) restraints added in 5.1 seconds 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 14 sheets defined 66.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.587A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.735A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.696A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.661A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.050A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.791A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.591A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.517A pdb=" N ASN A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.780A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.722A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.671A pdb=" N PHE A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.529A pdb=" N SER A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 466 removed outlier: 3.689A pdb=" N ILE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 493 Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.857A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 525 through 531 removed outlier: 4.598A pdb=" N ASN A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.701A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 removed outlier: 3.741A pdb=" N LEU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.774A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.901A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 629 Processing helix chain 'A' and resid 648 through 658 removed outlier: 4.160A pdb=" N HIS A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 removed outlier: 3.629A pdb=" N SER A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.626A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.868A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 841 through 845 removed outlier: 4.056A pdb=" N LEU A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 900 Processing helix chain 'A' and resid 911 through 922 removed outlier: 3.707A pdb=" N THR A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 933 removed outlier: 3.739A pdb=" N GLU A 931 " --> pdb=" O ASN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.538A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 removed outlier: 4.146A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 973 through 990 removed outlier: 3.759A pdb=" N LYS A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.668A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A1005 " --> pdb=" O MET A1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.654A pdb=" N THR B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.612A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.688A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 115 through 123 removed outlier: 4.064A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.539A pdb=" N GLY B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.701A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 197 removed outlier: 4.648A pdb=" N ASP B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 237 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.197A pdb=" N MET B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.989A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 302' Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.966A pdb=" N LYS B 331 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 467 through 494 removed outlier: 4.443A pdb=" N TYR B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 removed outlier: 4.045A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.957A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 removed outlier: 4.048A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 541 through 546 removed outlier: 4.245A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.686A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.748A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 629 removed outlier: 3.592A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.705A pdb=" N HIS B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.795A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.062A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.967A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.024A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 4.010A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 833 through 841 Processing helix chain 'B' and resid 848 through 857 removed outlier: 3.759A pdb=" N HIS B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 878 through 900 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.543A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 removed outlier: 3.941A pdb=" N LEU B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 removed outlier: 3.626A pdb=" N GLY B 972 " --> pdb=" O GLY B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 991 removed outlier: 4.280A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 removed outlier: 4.003A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.660A pdb=" N LEU D 73 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.553A pdb=" N THR E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.515A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 removed outlier: 3.740A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 115 through 125 Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 192 through 197 removed outlier: 3.810A pdb=" N TYR E 197 " --> pdb=" O TYR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.796A pdb=" N SER E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 237 removed outlier: 3.702A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.749A pdb=" N GLY E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 275 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 281 through 295 removed outlier: 4.204A pdb=" N ASP E 291 " --> pdb=" O SER E 287 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 328 through 332 removed outlier: 3.779A pdb=" N LYS E 331 " --> pdb=" O ILE E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 366 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 376 through 392 Processing helix chain 'E' and resid 411 through 416 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 448 through 457 removed outlier: 4.852A pdb=" N TYR E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 456 " --> pdb=" O TYR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 491 removed outlier: 3.808A pdb=" N ILE E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN E 483 " --> pdb=" O TYR E 479 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER E 484 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 486 " --> pdb=" O TYR E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 removed outlier: 3.991A pdb=" N THR E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 541 through 545 removed outlier: 3.555A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 572 Processing helix chain 'E' and resid 579 through 598 removed outlier: 4.078A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 598 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.771A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 626 Processing helix chain 'E' and resid 648 through 658 Processing helix chain 'E' and resid 660 through 670 Processing helix chain 'E' and resid 680 through 689 removed outlier: 3.510A pdb=" N ILE E 684 " --> pdb=" O GLU E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 698 Processing helix chain 'E' and resid 707 through 724 Processing helix chain 'E' and resid 730 through 742 Processing helix chain 'E' and resid 750 through 764 Processing helix chain 'E' and resid 768 through 777 removed outlier: 3.581A pdb=" N ILE E 772 " --> pdb=" O PRO E 768 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 774 " --> pdb=" O SER E 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 40 Processing helix chain 'G' and resid 48 through 54 removed outlier: 3.608A pdb=" N THR G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 72 Processing helix chain 'G' and resid 81 through 94 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 96 through 108 removed outlier: 4.386A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU G 104 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 removed outlier: 4.055A pdb=" N LYS G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 121 " --> pdb=" O ILE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 146 Processing helix chain 'G' and resid 157 through 161 removed outlier: 3.736A pdb=" N ALA G 161 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.538A pdb=" N TYR G 197 " --> pdb=" O TYR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 223 through 237 Processing helix chain 'G' and resid 254 through 264 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 316 through 322 removed outlier: 4.264A pdb=" N ALA G 321 " --> pdb=" O PRO G 318 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 322 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 333 removed outlier: 3.706A pdb=" N LYS G 331 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS G 332 " --> pdb=" O ASP G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 366 Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 374 through 391 Processing helix chain 'G' and resid 411 through 416 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'G' and resid 433 through 445 Processing helix chain 'G' and resid 447 through 462 Processing helix chain 'G' and resid 463 through 465 No H-bonds generated for 'chain 'G' and resid 463 through 465' Processing helix chain 'G' and resid 467 through 494 removed outlier: 4.245A pdb=" N TYR G 471 " --> pdb=" O ASN G 467 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G 494 " --> pdb=" O THR G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 519 Processing helix chain 'G' and resid 525 through 531 removed outlier: 4.004A pdb=" N ASN G 529 " --> pdb=" O ASP G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 539 Processing helix chain 'G' and resid 540 through 544 Processing helix chain 'G' and resid 551 through 552 No H-bonds generated for 'chain 'G' and resid 551 through 552' Processing helix chain 'G' and resid 554 through 554 No H-bonds generated for 'chain 'G' and resid 554 through 554' Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 580 through 596 Processing helix chain 'G' and resid 600 through 604 removed outlier: 4.038A pdb=" N VAL G 603 " --> pdb=" O LEU G 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 628 removed outlier: 3.738A pdb=" N ALA G 623 " --> pdb=" O LEU G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 658 removed outlier: 4.159A pdb=" N HIS G 658 " --> pdb=" O ASN G 654 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 671 removed outlier: 3.593A pdb=" N ILE G 664 " --> pdb=" O LYS G 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 701 removed outlier: 3.834A pdb=" N ALA G 701 " --> pdb=" O LYS G 697 " (cutoff:3.500A) Processing helix chain 'G' and resid 707 through 723 removed outlier: 4.286A pdb=" N GLN G 711 " --> pdb=" O VAL G 707 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE G 713 " --> pdb=" O TYR G 709 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 714 " --> pdb=" O THR G 710 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 716 " --> pdb=" O PHE G 712 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 718 " --> pdb=" O SER G 714 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA G 723 " --> pdb=" O ALA G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 743 Processing helix chain 'G' and resid 750 through 765 Processing helix chain 'G' and resid 770 through 786 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.070A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 130 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.803A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 197 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR C 171 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 11 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR C 24 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 13 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.803A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.290A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 244 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 246 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA7, first strand: chain 'D' and resid 67 through 68 removed outlier: 4.232A pdb=" N PHE D 67 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 24 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU D 21 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG D 15 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR D 171 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 197 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 68 removed outlier: 4.232A pdb=" N PHE D 67 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 24 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 42 through 46 removed outlier: 3.527A pdb=" N PHE E 244 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 574 through 575 removed outlier: 3.716A pdb=" N TYR E 574 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA F 30 " --> pdb=" O TYR E 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 150 through 152 removed outlier: 5.976A pdb=" N SER G 150 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS G 169 " --> pdb=" O SER G 150 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 152 " --> pdb=" O LYS G 169 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 129 " --> pdb=" O TYR G 166 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS G 128 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE G 213 " --> pdb=" O PHE G 244 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ILE G 246 " --> pdb=" O ILE G 213 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE G 215 " --> pdb=" O ILE G 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 338 through 340 Processing sheet with id=AB4, first strand: chain 'F' and resid 67 through 68 removed outlier: 4.320A pdb=" N PHE F 67 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR F 24 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR F 171 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN F 197 " --> pdb=" O TYR F 171 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 192 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 233 " --> pdb=" O GLN F 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 23 through 26 1578 hydrogen bonds defined for protein. 4536 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: 11.11 Time building geometry restraints manager: 12.57 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: 9078 1.34 - 1.46: 5564 1.46 - 1.57: 15333 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 30159 Sorted by residual: bond pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " ideal model delta sigma weight residual 1.534 1.547 -0.012 6.80e-03 2.16e+04 3.24e+00 bond pdb=" C ILE G 87 " pdb=" N PRO G 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.02e+00 bond pdb=" CA ILE G 87 " pdb=" C ILE G 87 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.97e+00 bond pdb=" C ILE B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.10e+00 bond pdb=" C ASP E 281 " pdb=" N TYR E 282 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.27e-02 6.20e+03 1.84e+00 ... (remaining 30154 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.89: 321 105.89 - 113.53: 15970 113.53 - 121.17: 16906 121.17 - 128.81: 7245 128.81 - 136.45: 148 Bond angle restraints: 40590 Sorted by residual: angle pdb=" C ARG G 86 " pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 120.24 125.76 -5.52 6.30e-01 2.52e+00 7.68e+01 angle pdb=" C PRO B 74 " pdb=" N LYS B 75 " pdb=" CA LYS B 75 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C ARG E 247 " pdb=" N THR E 248 " pdb=" CA THR E 248 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C MET G 124 " pdb=" N ASN G 125 " pdb=" CA ASN G 125 " ideal model delta sigma weight residual 121.80 132.22 -10.42 2.44e+00 1.68e-01 1.82e+01 angle pdb=" CA TYR B 282 " pdb=" CB TYR B 282 " pdb=" CG TYR B 282 " ideal model delta sigma weight residual 113.90 121.40 -7.50 1.80e+00 3.09e-01 1.73e+01 ... (remaining 40585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 15884 17.22 - 34.43: 1536 34.43 - 51.65: 416 51.65 - 68.86: 99 68.86 - 86.08: 10 Dihedral angle restraints: 17945 sinusoidal: 7369 harmonic: 10576 Sorted by residual: dihedral pdb=" CA PHE B 921 " pdb=" C PHE B 921 " pdb=" N LEU B 922 " pdb=" CA LEU B 922 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA SER B 287 " pdb=" C SER B 287 " pdb=" N ALA B 288 " pdb=" CA ALA B 288 " ideal model delta harmonic sigma weight residual 180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PHE E 550 " pdb=" C PHE E 550 " pdb=" N LEU E 551 " pdb=" CA LEU E 551 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2940 0.043 - 0.086: 1106 0.086 - 0.129: 247 0.129 - 0.171: 56 0.171 - 0.214: 2 Chirality restraints: 4351 Sorted by residual: chirality pdb=" CB THR E 562 " pdb=" CA THR E 562 " pdb=" OG1 THR E 562 " pdb=" CG2 THR E 562 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR E 248 " pdb=" N THR E 248 " pdb=" C THR E 248 " pdb=" CB THR E 248 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE G 275 " pdb=" CA ILE G 275 " pdb=" CG1 ILE G 275 " pdb=" CG2 ILE G 275 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 4348 not shown) Planarity restraints: 5159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 317 " 0.051 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO B 318 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 317 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO E 318 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 318 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 318 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 115 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO G 116 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 116 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 116 " 0.034 5.00e-02 4.00e+02 ... (remaining 5156 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4497 2.76 - 3.30: 29167 3.30 - 3.83: 52789 3.83 - 4.37: 60079 4.37 - 4.90: 96199 Nonbonded interactions: 242731 Sorted by model distance: nonbonded pdb=" OH TYR E 436 " pdb=" O VAL E 470 " model vdw 2.228 2.440 nonbonded pdb=" O GLU B 516 " pdb=" OG1 THR B 520 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR E 472 " pdb=" O LEU E 542 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR E 218 " pdb=" O ASP E 222 " model vdw 2.269 2.440 nonbonded pdb=" O VAL G 707 " pdb=" OG1 THR G 710 " model vdw 2.269 2.440 ... (remaining 242726 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 23 through 546 or resid 548 through 638 or resid 642 throu \ gh 830 or resid 832 through 843 or resid 847 through 1005)) selection = (chain 'B' and (resid 23 through 73 or resid 81 through 110 or (resid 111 throug \ h 113 and (name N or name CA or name C or name O or name CB )) or resid 114 thro \ ugh 160 or resid 165 through 269 or resid 279 through 801 or (resid 802 and (nam \ e N or name CA or name C or name O or name CB )) or resid 803 through 1005)) } ncs_group { reference = (chain 'C' and (resid 5 through 33 or resid 52 through 177 or resid 190 through \ 236)) selection = (chain 'D' and (resid 5 through 209 or resid 217 through 227 or (resid 228 throu \ gh 229 and (name N or name CA or name C or name O or name CB )) or resid 230 thr \ ough 235 or (resid 236 and (name N or name CA or name C or name O or name CB ))) \ ) } ncs_group { reference = (chain 'E' and (resid 22 through 179 or resid 186 through 217 or resid 222 throu \ gh 297 or resid 316 through 396 or resid 409 through 426 or resid 432 through 49 \ 8 or resid 502 or resid 507 through 553 or resid 555 through 573 or resid 580 th \ rough 627 or resid 649 through 672 or resid 682 through 727 or resid 730 through \ 766 or resid 769 through 777)) selection = (chain 'G' and (resid 22 through 71 or resid 80 through 110 or resid 112 through \ 125 or resid 130 through 145 or resid 165 through 343 or resid 347 through 353 \ or resid 355 through 372 or resid 375 through 498 or resid 517 or resid 522 or r \ esid 527 through 627 or resid 649 through 689 or resid 691 through 700 or resid \ 706 through 777)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.040 Extract box with map and model: 4.920 Check model and map are aligned: 0.260 Set scattering table: 0.300 Process input model: 77.620 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.003 0.052 30159 Z= 0.214 Angle : 0.700 11.453 40590 Z= 0.395 Chirality : 0.046 0.214 4351 Planarity : 0.005 0.076 5159 Dihedral : 14.999 86.081 11109 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.12 % Rotamer: Outliers : 5.17 % Allowed : 12.04 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 3455 helix: -1.17 (0.10), residues: 2022 sheet: -0.37 (0.37), residues: 218 loop : -1.60 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 601 HIS 0.008 0.001 HIS B 128 PHE 0.022 0.002 PHE A 559 TYR 0.018 0.002 TYR D 175 ARG 0.011 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 468 time to evaluate : 3.569 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: 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: 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: 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: symmetry clash REVERT: A 124 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8183 (tpp) REVERT: A 204 MET cc_start: 0.9637 (tmm) cc_final: 0.9191 (tmm) REVERT: A 226 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8663 (p0) REVERT: A 260 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: A 290 MET cc_start: 0.9604 (ttt) cc_final: 0.9347 (ttt) REVERT: A 421 MET cc_start: 0.9381 (ppp) cc_final: 0.9059 (ppp) REVERT: A 504 TYR cc_start: 0.7366 (t80) cc_final: 0.6997 (t80) REVERT: A 519 MET cc_start: 0.9134 (mmp) cc_final: 0.8387 (mmm) REVERT: A 524 ILE cc_start: 0.9515 (pt) cc_final: 0.8855 (mp) REVERT: A 527 LEU cc_start: 0.9509 (mt) cc_final: 0.9186 (mt) REVERT: A 557 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9063 (mtmm) REVERT: A 588 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9448 (tt) REVERT: A 660 LYS cc_start: 0.9377 (tptp) cc_final: 0.9052 (tptp) REVERT: A 662 ASP cc_start: 0.9146 (p0) cc_final: 0.8796 (p0) REVERT: A 693 GLU cc_start: 0.9403 (tp30) cc_final: 0.8652 (tp30) REVERT: A 704 MET cc_start: 0.7364 (ptp) cc_final: 0.6931 (ptp) REVERT: A 712 PHE cc_start: 0.9342 (t80) cc_final: 0.9009 (t80) REVERT: A 866 MET cc_start: 0.9488 (tmm) cc_final: 0.9256 (tmm) REVERT: A 913 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7931 (ppp) REVERT: A 938 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8241 (p0) REVERT: B 100 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: B 105 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9105 (mmmm) REVERT: B 183 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 315 LYS cc_start: 0.9308 (tttt) cc_final: 0.9014 (tttt) REVERT: B 331 LYS cc_start: 0.9571 (pttp) cc_final: 0.9353 (mtmm) REVERT: B 361 PHE cc_start: 0.9474 (m-80) cc_final: 0.8788 (m-10) REVERT: B 396 MET cc_start: 0.9002 (mpp) cc_final: 0.8749 (mpp) REVERT: B 412 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 441 PHE cc_start: 0.9498 (m-10) cc_final: 0.9222 (m-80) REVERT: B 448 TRP cc_start: 0.9121 (m-10) cc_final: 0.8879 (m-10) REVERT: B 525 ASP cc_start: 0.9426 (p0) cc_final: 0.9124 (p0) REVERT: B 540 LYS cc_start: 0.9196 (tmmt) cc_final: 0.8979 (tmtt) REVERT: B 553 ASP cc_start: 0.9544 (p0) cc_final: 0.9320 (p0) REVERT: B 616 MET cc_start: 0.9192 (ttm) cc_final: 0.8856 (ttm) REVERT: B 618 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9216 (mm) REVERT: B 759 GLU cc_start: 0.9677 (OUTLIER) cc_final: 0.9263 (mm-30) REVERT: B 915 THR cc_start: 0.9643 (OUTLIER) cc_final: 0.9361 (p) REVERT: B 959 LEU cc_start: 0.9724 (tp) cc_final: 0.9516 (tp) REVERT: B 975 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.7406 (p90) REVERT: B 976 MET cc_start: 0.8872 (mpp) cc_final: 0.8668 (mmt) REVERT: B 994 LYS cc_start: 0.9197 (mppt) cc_final: 0.8974 (mmtm) REVERT: B 997 LEU cc_start: 0.9719 (mt) cc_final: 0.9471 (tt) REVERT: C 67 PHE cc_start: 0.8892 (m-80) cc_final: 0.8593 (m-80) REVERT: D 63 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8814 (p) REVERT: D 192 TYR cc_start: 0.8700 (m-80) cc_final: 0.8456 (m-80) REVERT: D 231 MET cc_start: 0.8201 (pmm) cc_final: 0.7856 (pmm) REVERT: E 197 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: E 202 ASN cc_start: 0.9070 (t0) cc_final: 0.8800 (t0) REVERT: E 282 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: G 91 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7744 (t80) REVERT: G 202 ASN cc_start: 0.8846 (m110) cc_final: 0.8538 (t0) REVERT: G 396 MET cc_start: 0.6287 (mtt) cc_final: 0.6047 (mmt) REVERT: G 471 TYR cc_start: 0.7109 (t80) cc_final: 0.6725 (t80) REVERT: G 587 ARG cc_start: 0.9295 (tpp80) cc_final: 0.9051 (mmp80) REVERT: G 697 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8609 (ptmm) outliers start: 166 outliers final: 28 residues processed: 606 average time/residue: 0.4127 time to fit residues: 400.3086 Evaluate side-chains 355 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 309 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 148 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 276 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 192 ASN A 263 ASN A 351 ASN A 493 ASN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 HIS A 975 HIS B 78 ASN B 226 ASN B 461 ASN B 666 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 323 GLN E 332 HIS E 591 ASN ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN ** G 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 521 ASN G 666 ASN G 765 ASN G 782 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30159 Z= 0.208 Angle : 0.563 8.507 40590 Z= 0.311 Chirality : 0.041 0.171 4351 Planarity : 0.004 0.054 5159 Dihedral : 4.958 23.151 3886 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % 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: -0.68 (0.14), residues: 3455 helix: 0.12 (0.11), residues: 2100 sheet: -0.12 (0.36), residues: 210 loop : -1.44 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 143 HIS 0.010 0.001 HIS A 606 PHE 0.041 0.002 PHE G 91 TYR 0.030 0.002 TYR E 721 ARG 0.007 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 385 time to evaluate : 3.624 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: 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: 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 202 ASN cc_start: 0.9391 (t0) cc_final: 0.9179 (t0) REVERT: A 204 MET cc_start: 0.9619 (tmm) cc_final: 0.9304 (tmm) REVERT: A 290 MET cc_start: 0.9480 (ttt) cc_final: 0.8871 (ttm) REVERT: A 493 ASN cc_start: 0.9475 (m110) cc_final: 0.9109 (p0) REVERT: A 519 MET cc_start: 0.9248 (mmp) cc_final: 0.8866 (mmm) REVERT: A 524 ILE cc_start: 0.9585 (pt) cc_final: 0.9028 (mm) REVERT: A 527 LEU cc_start: 0.9604 (mt) cc_final: 0.9296 (mt) REVERT: A 531 MET cc_start: 0.9033 (mmm) cc_final: 0.8829 (mmm) REVERT: A 557 LYS cc_start: 0.9540 (mtmm) cc_final: 0.9095 (mttt) REVERT: A 578 MET cc_start: 0.8807 (ppp) cc_final: 0.8569 (ppp) REVERT: A 620 ILE cc_start: 0.9924 (pt) cc_final: 0.9697 (pt) REVERT: A 647 MET cc_start: 0.9231 (mmp) cc_final: 0.8833 (mmm) REVERT: A 693 GLU cc_start: 0.9438 (tp30) cc_final: 0.8904 (tp30) REVERT: A 704 MET cc_start: 0.7182 (ptp) cc_final: 0.6682 (ptp) REVERT: A 712 PHE cc_start: 0.9397 (t80) cc_final: 0.9113 (t80) REVERT: A 866 MET cc_start: 0.9424 (tmm) cc_final: 0.8943 (tmm) REVERT: B 168 LEU cc_start: 0.9605 (tp) cc_final: 0.9368 (tp) REVERT: B 315 LYS cc_start: 0.9372 (tttt) cc_final: 0.8993 (tttt) REVERT: B 361 PHE cc_start: 0.9425 (m-80) cc_final: 0.9004 (m-80) REVERT: B 434 ASP cc_start: 0.9602 (m-30) cc_final: 0.9060 (t70) REVERT: B 441 PHE cc_start: 0.9646 (m-10) cc_final: 0.9055 (m-80) REVERT: B 448 TRP cc_start: 0.8951 (m-10) cc_final: 0.8693 (m-10) REVERT: B 531 MET cc_start: 0.8749 (mmm) cc_final: 0.8544 (mmt) REVERT: B 553 ASP cc_start: 0.9648 (p0) cc_final: 0.9367 (p0) REVERT: B 759 GLU cc_start: 0.9862 (mm-30) cc_final: 0.9609 (mm-30) REVERT: B 776 ASP cc_start: 0.9160 (t70) cc_final: 0.8894 (t0) REVERT: C 67 PHE cc_start: 0.9012 (m-80) cc_final: 0.8674 (m-80) REVERT: D 192 TYR cc_start: 0.8739 (m-80) cc_final: 0.8511 (m-80) REVERT: D 231 MET cc_start: 0.8354 (pmm) cc_final: 0.7901 (pmm) REVERT: E 197 TYR cc_start: 0.8092 (m-80) cc_final: 0.7868 (m-80) REVERT: E 261 TYR cc_start: 0.8213 (m-10) cc_final: 0.7747 (m-80) REVERT: E 290 MET cc_start: 0.8854 (ptt) cc_final: 0.8312 (ppp) REVERT: E 578 MET cc_start: 0.8547 (tmm) cc_final: 0.8331 (tmm) REVERT: G 202 ASN cc_start: 0.8704 (m110) cc_final: 0.8375 (t0) REVERT: G 471 TYR cc_start: 0.7238 (t80) cc_final: 0.6949 (t80) REVERT: G 594 PHE cc_start: 0.9207 (t80) cc_final: 0.8887 (t80) outliers start: 1 outliers final: 0 residues processed: 386 average time/residue: 0.4306 time to fit residues: 262.3327 Evaluate side-chains 262 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 266 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 321 optimal weight: 0.6980 chunk 346 optimal weight: 40.0000 chunk 286 optimal weight: 8.9990 chunk 318 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 HIS ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 HIS ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30159 Z= 0.192 Angle : 0.536 8.424 40590 Z= 0.293 Chirality : 0.040 0.159 4351 Planarity : 0.004 0.052 5159 Dihedral : 4.758 21.165 3886 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.37 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3455 helix: 0.55 (0.11), residues: 2099 sheet: -0.10 (0.36), residues: 209 loop : -1.34 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 448 HIS 0.010 0.001 HIS B 810 PHE 0.018 0.002 PHE E 240 TYR 0.027 0.001 TYR E 721 ARG 0.005 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.452 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: 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: symmetry clash REVERT: A 124 MET cc_start: 0.8813 (tpp) cc_final: 0.8192 (tpp) REVERT: A 202 ASN cc_start: 0.9333 (t0) cc_final: 0.9048 (t0) REVERT: A 204 MET cc_start: 0.9607 (tmm) cc_final: 0.9314 (tmm) REVERT: A 290 MET cc_start: 0.9484 (ttt) cc_final: 0.8895 (ttm) REVERT: A 519 MET cc_start: 0.9350 (mmp) cc_final: 0.9086 (mmm) REVERT: A 524 ILE cc_start: 0.9558 (pt) cc_final: 0.8932 (mm) REVERT: A 527 LEU cc_start: 0.9568 (mt) cc_final: 0.9315 (mt) REVERT: A 531 MET cc_start: 0.9120 (mmm) cc_final: 0.8604 (mmm) REVERT: A 543 GLU cc_start: 0.9545 (pm20) cc_final: 0.9313 (pm20) REVERT: A 550 PHE cc_start: 0.9513 (t80) cc_final: 0.9311 (t80) REVERT: A 647 MET cc_start: 0.9231 (mmp) cc_final: 0.9000 (mmm) REVERT: A 693 GLU cc_start: 0.9426 (tp30) cc_final: 0.8898 (tp30) REVERT: A 704 MET cc_start: 0.7194 (ptp) cc_final: 0.6799 (ptp) REVERT: A 712 PHE cc_start: 0.9393 (t80) cc_final: 0.9131 (t80) REVERT: A 743 TYR cc_start: 0.8625 (m-80) cc_final: 0.8414 (m-80) REVERT: A 866 MET cc_start: 0.9449 (tmm) cc_final: 0.8980 (tmm) REVERT: A 913 MET cc_start: 0.7793 (ppp) cc_final: 0.7316 (ppp) REVERT: B 315 LYS cc_start: 0.9438 (tttt) cc_final: 0.9021 (tttt) REVERT: B 361 PHE cc_start: 0.9361 (m-80) cc_final: 0.8799 (m-80) REVERT: B 434 ASP cc_start: 0.9600 (m-30) cc_final: 0.8993 (t70) REVERT: B 441 PHE cc_start: 0.9635 (m-10) cc_final: 0.9061 (m-80) REVERT: B 521 ASN cc_start: 0.8893 (m-40) cc_final: 0.8645 (m-40) REVERT: B 531 MET cc_start: 0.9236 (mmm) cc_final: 0.8686 (mmt) REVERT: B 553 ASP cc_start: 0.9643 (p0) cc_final: 0.9374 (p0) REVERT: B 759 GLU cc_start: 0.9856 (mm-30) cc_final: 0.9589 (mm-30) REVERT: B 776 ASP cc_start: 0.9155 (t70) cc_final: 0.8933 (t0) REVERT: C 67 PHE cc_start: 0.9000 (m-80) cc_final: 0.8729 (m-80) REVERT: C 219 LYS cc_start: 0.9004 (tptp) cc_final: 0.8797 (tptp) REVERT: D 231 MET cc_start: 0.8372 (pmm) cc_final: 0.7910 (pmm) REVERT: E 202 ASN cc_start: 0.8967 (t0) cc_final: 0.8606 (t0) REVERT: E 261 TYR cc_start: 0.8254 (m-10) cc_final: 0.7805 (m-80) REVERT: E 290 MET cc_start: 0.8906 (ptt) cc_final: 0.8467 (ppp) REVERT: G 202 ASN cc_start: 0.8686 (m110) cc_final: 0.8351 (t0) REVERT: G 227 MET cc_start: 0.8937 (tmm) cc_final: 0.8689 (tmm) REVERT: G 471 TYR cc_start: 0.7241 (t80) cc_final: 0.6913 (t80) REVERT: G 594 PHE cc_start: 0.9213 (t80) cc_final: 0.8789 (t80) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.4207 time to fit residues: 243.1079 Evaluate side-chains 247 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 322 optimal weight: 9.9990 chunk 341 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 HIS ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS B 109 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN ** E 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 467 ASN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30159 Z= 0.223 Angle : 0.550 8.265 40590 Z= 0.302 Chirality : 0.040 0.147 4351 Planarity : 0.004 0.050 5159 Dihedral : 4.752 21.363 3886 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.83 % Favored : 95.05 % Rotamer: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % 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: -0.10 (0.14), residues: 3455 helix: 0.66 (0.11), residues: 2102 sheet: -0.09 (0.36), residues: 209 loop : -1.33 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 601 HIS 0.007 0.001 HIS B 975 PHE 0.033 0.002 PHE E 240 TYR 0.019 0.002 TYR E 260 ARG 0.005 0.000 ARG A 987 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 3.419 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8901 (tpp) cc_final: 0.8371 (tpp) REVERT: A 202 ASN cc_start: 0.9337 (t0) cc_final: 0.9045 (t0) REVERT: A 204 MET cc_start: 0.9568 (tmm) cc_final: 0.9145 (tmm) REVERT: A 290 MET cc_start: 0.9508 (ttt) cc_final: 0.8921 (ttm) REVERT: A 519 MET cc_start: 0.9360 (mmp) cc_final: 0.9140 (mmt) REVERT: A 524 ILE cc_start: 0.9571 (pt) cc_final: 0.9349 (pt) REVERT: A 543 GLU cc_start: 0.9550 (pm20) cc_final: 0.9330 (pm20) REVERT: A 647 MET cc_start: 0.9309 (mmp) cc_final: 0.9030 (mmm) REVERT: A 693 GLU cc_start: 0.9388 (tp30) cc_final: 0.8803 (tp30) REVERT: A 704 MET cc_start: 0.7233 (ptp) cc_final: 0.6847 (ptp) REVERT: A 712 PHE cc_start: 0.9402 (t80) cc_final: 0.9159 (t80) REVERT: A 866 MET cc_start: 0.9458 (tmm) cc_final: 0.9026 (tmm) REVERT: B 315 LYS cc_start: 0.9426 (tttt) cc_final: 0.9067 (tttt) REVERT: B 361 PHE cc_start: 0.9361 (m-80) cc_final: 0.8775 (m-80) REVERT: B 434 ASP cc_start: 0.9609 (m-30) cc_final: 0.9006 (t70) REVERT: B 441 PHE cc_start: 0.9631 (m-10) cc_final: 0.9093 (m-80) REVERT: B 448 TRP cc_start: 0.8915 (m-10) cc_final: 0.8668 (m-10) REVERT: B 531 MET cc_start: 0.9158 (mmm) cc_final: 0.8487 (mmt) REVERT: B 553 ASP cc_start: 0.9644 (p0) cc_final: 0.9419 (p0) REVERT: B 647 MET cc_start: 0.7892 (ppp) cc_final: 0.7195 (ppp) REVERT: B 759 GLU cc_start: 0.9849 (mm-30) cc_final: 0.9602 (mm-30) REVERT: B 913 MET cc_start: 0.9610 (ptm) cc_final: 0.8817 (ppp) REVERT: B 916 PHE cc_start: 0.9160 (m-10) cc_final: 0.8945 (m-10) REVERT: C 67 PHE cc_start: 0.9109 (m-80) cc_final: 0.8868 (m-80) REVERT: D 231 MET cc_start: 0.8417 (pmm) cc_final: 0.8002 (pmm) REVERT: E 202 ASN cc_start: 0.8999 (t0) cc_final: 0.8623 (t0) REVERT: E 261 TYR cc_start: 0.8334 (m-10) cc_final: 0.7850 (m-80) REVERT: E 569 MET cc_start: 0.8856 (ppp) cc_final: 0.8612 (ppp) REVERT: E 691 ILE cc_start: 0.8674 (mm) cc_final: 0.8430 (pt) REVERT: G 202 ASN cc_start: 0.8654 (m110) cc_final: 0.8403 (t0) REVERT: G 227 MET cc_start: 0.8978 (tmm) cc_final: 0.8716 (tmm) REVERT: G 357 MET cc_start: 0.9187 (mmm) cc_final: 0.8752 (mmm) REVERT: G 471 TYR cc_start: 0.7055 (t80) cc_final: 0.6818 (t80) REVERT: G 594 PHE cc_start: 0.9230 (t80) cc_final: 0.8775 (t80) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.4405 time to fit residues: 245.8755 Evaluate side-chains 248 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 235 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.0970 chunk 306 optimal weight: 0.0370 chunk 86 optimal weight: 20.0000 overall best weight: 1.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 HIS ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 HIS E 351 ASN E 493 ASN ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30159 Z= 0.132 Angle : 0.496 9.605 40590 Z= 0.264 Chirality : 0.040 0.199 4351 Planarity : 0.003 0.068 5159 Dihedral : 4.502 21.708 3886 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.20 (0.14), residues: 3455 helix: 0.93 (0.11), residues: 2106 sheet: -0.08 (0.36), residues: 207 loop : -1.27 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 59 HIS 0.008 0.001 HIS A 658 PHE 0.035 0.001 PHE G 91 TYR 0.021 0.001 TYR G 92 ARG 0.004 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.274 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: 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 59 TRP cc_start: 0.8802 (t-100) cc_final: 0.8533 (t-100) REVERT: A 124 MET cc_start: 0.8534 (tpp) cc_final: 0.8164 (tpp) REVERT: A 204 MET cc_start: 0.9588 (tmm) cc_final: 0.9324 (tmm) REVERT: A 290 MET cc_start: 0.9435 (ttt) cc_final: 0.9015 (ttm) REVERT: A 519 MET cc_start: 0.9315 (mmp) cc_final: 0.9030 (mmt) REVERT: A 543 GLU cc_start: 0.9527 (pm20) cc_final: 0.9321 (pm20) REVERT: A 578 MET cc_start: 0.8928 (ppp) cc_final: 0.8461 (ppp) REVERT: A 647 MET cc_start: 0.9145 (mmp) cc_final: 0.8895 (mmm) REVERT: A 693 GLU cc_start: 0.9401 (tp30) cc_final: 0.8822 (tp30) REVERT: A 704 MET cc_start: 0.7223 (ptp) cc_final: 0.6876 (ptp) REVERT: A 712 PHE cc_start: 0.9348 (t80) cc_final: 0.9088 (t80) REVERT: A 743 TYR cc_start: 0.8691 (m-80) cc_final: 0.8474 (m-80) REVERT: A 866 MET cc_start: 0.9432 (tmm) cc_final: 0.8938 (tmm) REVERT: B 204 MET cc_start: 0.9272 (tmm) cc_final: 0.9069 (tmm) REVERT: B 307 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9268 (mt-10) REVERT: B 315 LYS cc_start: 0.9455 (tttt) cc_final: 0.9104 (tttt) REVERT: B 361 PHE cc_start: 0.9294 (m-80) cc_final: 0.8698 (m-80) REVERT: B 375 LYS cc_start: 0.8996 (mmpt) cc_final: 0.8569 (mmmt) REVERT: B 434 ASP cc_start: 0.9602 (m-30) cc_final: 0.8894 (t70) REVERT: B 441 PHE cc_start: 0.9621 (m-10) cc_final: 0.9067 (m-80) REVERT: B 448 TRP cc_start: 0.8852 (m-10) cc_final: 0.8613 (m-10) REVERT: B 531 MET cc_start: 0.9183 (mmm) cc_final: 0.8859 (mmt) REVERT: B 553 ASP cc_start: 0.9636 (p0) cc_final: 0.9350 (p0) REVERT: B 776 ASP cc_start: 0.8680 (t0) cc_final: 0.8468 (t0) REVERT: B 913 MET cc_start: 0.9559 (ptm) cc_final: 0.8716 (ppp) REVERT: C 195 PHE cc_start: 0.9519 (m-80) cc_final: 0.8877 (m-80) REVERT: C 219 LYS cc_start: 0.9071 (tptp) cc_final: 0.8833 (tptp) REVERT: D 231 MET cc_start: 0.8354 (pmm) cc_final: 0.7913 (pmm) REVERT: E 202 ASN cc_start: 0.8934 (t0) cc_final: 0.8524 (t0) REVERT: E 261 TYR cc_start: 0.8377 (m-10) cc_final: 0.7765 (m-80) REVERT: E 290 MET cc_start: 0.8928 (ptt) cc_final: 0.8456 (ppp) REVERT: E 569 MET cc_start: 0.8900 (ppp) cc_final: 0.8680 (ppp) REVERT: G 202 ASN cc_start: 0.8621 (m110) cc_final: 0.8338 (t0) REVERT: G 227 MET cc_start: 0.8911 (tmm) cc_final: 0.8633 (tmm) REVERT: G 357 MET cc_start: 0.9240 (mmm) cc_final: 0.8788 (mmm) REVERT: G 471 TYR cc_start: 0.7142 (t80) cc_final: 0.6789 (t80) REVERT: G 594 PHE cc_start: 0.9169 (t80) cc_final: 0.8822 (t80) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.4234 time to fit residues: 246.9789 Evaluate side-chains 254 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 179 optimal weight: 0.0970 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 HIS ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN E 351 ASN ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30159 Z= 0.169 Angle : 0.511 8.301 40590 Z= 0.275 Chirality : 0.040 0.171 4351 Planarity : 0.003 0.060 5159 Dihedral : 4.460 20.844 3886 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % 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: 0.23 (0.14), residues: 3455 helix: 0.96 (0.11), residues: 2113 sheet: 0.05 (0.36), residues: 209 loop : -1.32 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 601 HIS 0.004 0.001 HIS A 658 PHE 0.026 0.001 PHE G 91 TYR 0.030 0.001 TYR B 755 ARG 0.006 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 3.600 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: 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 59 TRP cc_start: 0.8791 (t-100) cc_final: 0.8220 (t-100) REVERT: A 124 MET cc_start: 0.8663 (tpp) cc_final: 0.8431 (tpp) REVERT: A 202 ASN cc_start: 0.9188 (t0) cc_final: 0.8948 (t0) REVERT: A 204 MET cc_start: 0.9605 (tmm) cc_final: 0.9343 (tmm) REVERT: A 290 MET cc_start: 0.9469 (ttt) cc_final: 0.9108 (ttt) REVERT: A 519 MET cc_start: 0.9323 (mmp) cc_final: 0.9070 (mmt) REVERT: A 524 ILE cc_start: 0.9532 (pt) cc_final: 0.9288 (pt) REVERT: A 543 GLU cc_start: 0.9531 (pm20) cc_final: 0.9326 (pm20) REVERT: A 557 LYS cc_start: 0.9540 (mtmm) cc_final: 0.9003 (ptpp) REVERT: A 578 MET cc_start: 0.8939 (ppp) cc_final: 0.8460 (ppp) REVERT: A 647 MET cc_start: 0.9191 (mmp) cc_final: 0.8852 (mmm) REVERT: A 693 GLU cc_start: 0.9394 (tp30) cc_final: 0.8823 (tp30) REVERT: A 704 MET cc_start: 0.7384 (ptp) cc_final: 0.7082 (ptp) REVERT: A 712 PHE cc_start: 0.9358 (t80) cc_final: 0.9120 (t80) REVERT: A 743 TYR cc_start: 0.8767 (m-80) cc_final: 0.8535 (m-80) REVERT: A 866 MET cc_start: 0.9451 (tmm) cc_final: 0.8975 (tmm) REVERT: B 204 MET cc_start: 0.9296 (tmm) cc_final: 0.9023 (tmm) REVERT: B 307 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9273 (mt-10) REVERT: B 315 LYS cc_start: 0.9451 (tttt) cc_final: 0.9065 (tttt) REVERT: B 361 PHE cc_start: 0.9349 (m-80) cc_final: 0.8784 (m-80) REVERT: B 375 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8599 (mmmt) REVERT: B 434 ASP cc_start: 0.9590 (m-30) cc_final: 0.8952 (t70) REVERT: B 441 PHE cc_start: 0.9630 (m-10) cc_final: 0.9085 (m-80) REVERT: B 448 TRP cc_start: 0.8875 (m-10) cc_final: 0.8631 (m-10) REVERT: B 531 MET cc_start: 0.9213 (mmm) cc_final: 0.8873 (mmt) REVERT: B 553 ASP cc_start: 0.9638 (p0) cc_final: 0.9398 (p0) REVERT: B 647 MET cc_start: 0.7516 (ppp) cc_final: 0.6044 (ppp) REVERT: B 776 ASP cc_start: 0.8655 (t0) cc_final: 0.8442 (t0) REVERT: B 913 MET cc_start: 0.9550 (ptm) cc_final: 0.8795 (ppp) REVERT: D 231 MET cc_start: 0.8374 (pmm) cc_final: 0.7935 (pmm) REVERT: E 202 ASN cc_start: 0.8965 (t0) cc_final: 0.8539 (t0) REVERT: E 261 TYR cc_start: 0.8524 (m-10) cc_final: 0.7936 (m-80) REVERT: E 290 MET cc_start: 0.8966 (ptt) cc_final: 0.8491 (ppp) REVERT: E 531 MET cc_start: 0.8034 (tpp) cc_final: 0.7831 (tpp) REVERT: G 202 ASN cc_start: 0.8570 (m110) cc_final: 0.8348 (t0) REVERT: G 227 MET cc_start: 0.8933 (tmm) cc_final: 0.8670 (tmm) REVERT: G 357 MET cc_start: 0.9322 (mmm) cc_final: 0.8969 (mmm) REVERT: G 471 TYR cc_start: 0.6927 (t80) cc_final: 0.6519 (t80) REVERT: G 594 PHE cc_start: 0.9144 (t80) cc_final: 0.8834 (t80) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.4067 time to fit residues: 233.7411 Evaluate side-chains 254 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 249 optimal weight: 0.0980 chunk 193 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 340 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 HIS A 910 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN E 591 ASN ** E 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30159 Z= 0.144 Angle : 0.505 8.934 40590 Z= 0.268 Chirality : 0.040 0.168 4351 Planarity : 0.003 0.056 5159 Dihedral : 4.382 20.486 3886 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 0.37 (0.15), residues: 3455 helix: 1.07 (0.11), residues: 2113 sheet: 0.09 (0.37), residues: 209 loop : -1.24 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 757 HIS 0.007 0.001 HIS A 658 PHE 0.027 0.001 PHE G 659 TYR 0.021 0.001 TYR B 755 ARG 0.004 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 3.689 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: 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 59 TRP cc_start: 0.8798 (t-100) cc_final: 0.8239 (t-100) REVERT: A 124 MET cc_start: 0.8628 (tpp) cc_final: 0.8402 (tpp) REVERT: A 202 ASN cc_start: 0.9161 (t0) cc_final: 0.8251 (t0) REVERT: A 204 MET cc_start: 0.9598 (tmm) cc_final: 0.9305 (tmm) REVERT: A 290 MET cc_start: 0.9469 (ttt) cc_final: 0.9113 (ttt) REVERT: A 519 MET cc_start: 0.9330 (mmp) cc_final: 0.9082 (mmt) REVERT: A 524 ILE cc_start: 0.9556 (pt) cc_final: 0.9325 (pt) REVERT: A 527 LEU cc_start: 0.9657 (mt) cc_final: 0.9420 (mt) REVERT: A 531 MET cc_start: 0.9203 (mmm) cc_final: 0.8652 (mmm) REVERT: A 557 LYS cc_start: 0.9545 (mtmm) cc_final: 0.8980 (ptpp) REVERT: A 578 MET cc_start: 0.8884 (ppp) cc_final: 0.8424 (ppp) REVERT: A 647 MET cc_start: 0.9221 (mmp) cc_final: 0.8944 (mmm) REVERT: A 693 GLU cc_start: 0.9395 (tp30) cc_final: 0.8805 (tp30) REVERT: A 704 MET cc_start: 0.7195 (ptp) cc_final: 0.6884 (ptp) REVERT: A 712 PHE cc_start: 0.9342 (t80) cc_final: 0.9104 (t80) REVERT: A 743 TYR cc_start: 0.8760 (m-80) cc_final: 0.8513 (m-80) REVERT: A 866 MET cc_start: 0.9431 (tmm) cc_final: 0.8945 (tmm) REVERT: A 1001 MET cc_start: 0.9254 (tmm) cc_final: 0.9048 (tmm) REVERT: B 202 ASN cc_start: 0.8989 (m110) cc_final: 0.8692 (t0) REVERT: B 307 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9251 (mt-10) REVERT: B 315 LYS cc_start: 0.9449 (tttt) cc_final: 0.9084 (tttt) REVERT: B 361 PHE cc_start: 0.9350 (m-80) cc_final: 0.8781 (m-80) REVERT: B 375 LYS cc_start: 0.8974 (mmpt) cc_final: 0.8584 (mmmt) REVERT: B 434 ASP cc_start: 0.9602 (m-30) cc_final: 0.8933 (t70) REVERT: B 441 PHE cc_start: 0.9627 (m-10) cc_final: 0.9071 (m-80) REVERT: B 448 TRP cc_start: 0.8866 (m-10) cc_final: 0.8613 (m-10) REVERT: B 531 MET cc_start: 0.9220 (mmm) cc_final: 0.8882 (mmt) REVERT: B 553 ASP cc_start: 0.9632 (p0) cc_final: 0.9381 (p0) REVERT: B 595 LEU cc_start: 0.9546 (mt) cc_final: 0.9334 (mt) REVERT: B 647 MET cc_start: 0.7585 (ppp) cc_final: 0.6287 (ppp) REVERT: B 913 MET cc_start: 0.9555 (ptm) cc_final: 0.8789 (ppp) REVERT: C 67 PHE cc_start: 0.8997 (m-80) cc_final: 0.8796 (m-80) REVERT: D 231 MET cc_start: 0.8358 (pmm) cc_final: 0.7909 (pmm) REVERT: E 202 ASN cc_start: 0.8929 (t0) cc_final: 0.8491 (t0) REVERT: E 261 TYR cc_start: 0.8486 (m-10) cc_final: 0.7884 (m-80) REVERT: E 290 MET cc_start: 0.8926 (ptt) cc_final: 0.8471 (ppp) REVERT: E 357 MET cc_start: 0.9122 (tpt) cc_final: 0.8611 (ttt) REVERT: E 616 MET cc_start: 0.8026 (tpt) cc_final: 0.7755 (mtp) REVERT: E 691 ILE cc_start: 0.8609 (mm) cc_final: 0.8374 (pt) REVERT: G 202 ASN cc_start: 0.8585 (m110) cc_final: 0.8306 (t0) REVERT: G 357 MET cc_start: 0.9309 (mmm) cc_final: 0.8914 (mmm) REVERT: G 471 TYR cc_start: 0.6920 (t80) cc_final: 0.6512 (t80) REVERT: G 594 PHE cc_start: 0.9068 (t80) cc_final: 0.8812 (t80) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.3953 time to fit residues: 225.1418 Evaluate side-chains 252 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 216 optimal weight: 30.0000 chunk 231 optimal weight: 0.8980 chunk 168 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 HIS A 978 HIS ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 457 ASN ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30159 Z= 0.140 Angle : 0.506 8.792 40590 Z= 0.266 Chirality : 0.040 0.170 4351 Planarity : 0.003 0.055 5159 Dihedral : 4.325 20.072 3886 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.45 (0.15), residues: 3455 helix: 1.12 (0.11), residues: 2113 sheet: 0.00 (0.36), residues: 223 loop : -1.19 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 757 HIS 0.012 0.001 HIS A 978 PHE 0.024 0.001 PHE A 659 TYR 0.024 0.001 TYR B 721 ARG 0.006 0.000 ARG H 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 3.450 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: 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: symmetry clash REVERT: A 59 TRP cc_start: 0.8745 (t-100) cc_final: 0.8217 (t-100) REVERT: A 124 MET cc_start: 0.8616 (tpp) cc_final: 0.8370 (tpp) REVERT: A 202 ASN cc_start: 0.9152 (t0) cc_final: 0.8195 (t0) REVERT: A 204 MET cc_start: 0.9592 (tmm) cc_final: 0.9342 (tmm) REVERT: A 290 MET cc_start: 0.9461 (ttt) cc_final: 0.9114 (ttt) REVERT: A 335 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8871 (tm-30) REVERT: A 519 MET cc_start: 0.9332 (mmp) cc_final: 0.9095 (mmt) REVERT: A 524 ILE cc_start: 0.9546 (pt) cc_final: 0.9313 (pt) REVERT: A 527 LEU cc_start: 0.9656 (mt) cc_final: 0.9423 (mt) REVERT: A 531 MET cc_start: 0.9207 (mmm) cc_final: 0.8662 (mmm) REVERT: A 578 MET cc_start: 0.8945 (ppp) cc_final: 0.8456 (ppp) REVERT: A 636 PHE cc_start: 0.8823 (t80) cc_final: 0.8595 (t80) REVERT: A 647 MET cc_start: 0.9239 (mmp) cc_final: 0.8935 (mmm) REVERT: A 693 GLU cc_start: 0.9385 (tp30) cc_final: 0.8784 (tp30) REVERT: A 704 MET cc_start: 0.7185 (ptp) cc_final: 0.6873 (ptp) REVERT: A 712 PHE cc_start: 0.9345 (t80) cc_final: 0.9132 (t80) REVERT: A 743 TYR cc_start: 0.8761 (m-80) cc_final: 0.8513 (m-80) REVERT: A 866 MET cc_start: 0.9428 (tmm) cc_final: 0.8945 (tmm) REVERT: A 1001 MET cc_start: 0.9286 (tmm) cc_final: 0.8964 (tmm) REVERT: B 105 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8447 (mmmt) REVERT: B 202 ASN cc_start: 0.8993 (m110) cc_final: 0.8735 (t0) REVERT: B 315 LYS cc_start: 0.9443 (tttt) cc_final: 0.9036 (tttt) REVERT: B 361 PHE cc_start: 0.9353 (m-80) cc_final: 0.8768 (m-80) REVERT: B 375 LYS cc_start: 0.8963 (mmpt) cc_final: 0.8564 (mmmt) REVERT: B 434 ASP cc_start: 0.9586 (m-30) cc_final: 0.8931 (t70) REVERT: B 441 PHE cc_start: 0.9623 (m-10) cc_final: 0.9068 (m-80) REVERT: B 448 TRP cc_start: 0.9009 (m-10) cc_final: 0.8806 (m-10) REVERT: B 531 MET cc_start: 0.9310 (mmm) cc_final: 0.8898 (mmt) REVERT: B 553 ASP cc_start: 0.9630 (p0) cc_final: 0.9366 (p0) REVERT: B 595 LEU cc_start: 0.9537 (mt) cc_final: 0.9298 (mt) REVERT: B 647 MET cc_start: 0.7583 (ppp) cc_final: 0.6255 (ppp) REVERT: B 786 HIS cc_start: 0.8290 (t-90) cc_final: 0.7566 (t-170) REVERT: B 913 MET cc_start: 0.9525 (ptm) cc_final: 0.8784 (ppp) REVERT: B 936 MET cc_start: 0.8728 (mmp) cc_final: 0.8429 (mmp) REVERT: D 231 MET cc_start: 0.8343 (pmm) cc_final: 0.7877 (pmm) REVERT: E 202 ASN cc_start: 0.8946 (t0) cc_final: 0.8482 (t0) REVERT: E 261 TYR cc_start: 0.8422 (m-10) cc_final: 0.7838 (m-80) REVERT: E 290 MET cc_start: 0.8929 (ptt) cc_final: 0.8480 (ppp) REVERT: G 98 MET cc_start: 0.8447 (tpp) cc_final: 0.7681 (tpp) REVERT: G 357 MET cc_start: 0.9290 (mmm) cc_final: 0.8896 (mmm) REVERT: G 471 TYR cc_start: 0.6960 (t80) cc_final: 0.6558 (t80) REVERT: G 594 PHE cc_start: 0.9059 (t80) cc_final: 0.8823 (t80) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.4027 time to fit residues: 230.4305 Evaluate side-chains 254 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2772 > 50: distance: 40 - 65: 29.155 distance: 58 - 65: 31.908 distance: 65 - 66: 13.789 distance: 66 - 67: 10.800 distance: 66 - 69: 29.363 distance: 67 - 68: 55.562 distance: 67 - 74: 57.568 distance: 69 - 70: 35.005 distance: 70 - 71: 56.529 distance: 71 - 72: 56.727 distance: 72 - 73: 56.760 distance: 74 - 75: 54.738 distance: 75 - 76: 55.884 distance: 75 - 78: 43.855 distance: 76 - 77: 23.535 distance: 78 - 79: 39.718 distance: 79 - 80: 8.577 distance: 79 - 81: 38.136 distance: 82 - 83: 12.042 distance: 83 - 84: 63.846 distance: 83 - 86: 27.126 distance: 84 - 85: 56.276 distance: 84 - 88: 57.285 distance: 86 - 87: 33.790 distance: 88 - 89: 45.449 distance: 89 - 90: 53.967 distance: 89 - 92: 44.973 distance: 90 - 91: 55.464 distance: 90 - 99: 66.164 distance: 92 - 93: 25.675 distance: 93 - 95: 48.116 distance: 95 - 97: 13.351 distance: 96 - 98: 42.555 distance: 97 - 98: 35.372 distance: 99 - 100: 33.972 distance: 100 - 101: 56.702 distance: 100 - 103: 42.555 distance: 101 - 102: 39.436 distance: 101 - 109: 41.255 distance: 103 - 104: 14.646 distance: 104 - 105: 38.981 distance: 104 - 106: 50.773 distance: 105 - 107: 39.407 distance: 106 - 108: 33.809 distance: 107 - 108: 30.793 distance: 109 - 110: 56.693 distance: 110 - 113: 39.696 distance: 111 - 118: 40.536 distance: 113 - 114: 50.994 distance: 114 - 115: 41.065 distance: 115 - 116: 29.975 distance: 116 - 117: 49.842 distance: 118 - 119: 59.463 distance: 118 - 124: 56.768 distance: 119 - 120: 57.058 distance: 119 - 122: 20.515 distance: 120 - 121: 30.854 distance: 120 - 125: 56.702 distance: 122 - 123: 9.594 distance: 125 - 126: 58.624 distance: 126 - 127: 59.547 distance: 126 - 129: 30.533 distance: 127 - 128: 47.713 distance: 127 - 136: 26.965 distance: 129 - 130: 21.656 distance: 130 - 131: 39.937 distance: 130 - 132: 44.669 distance: 131 - 133: 45.757 distance: 132 - 134: 37.306 distance: 133 - 135: 44.826 distance: 134 - 135: 41.972 distance: 136 - 137: 55.130 distance: 137 - 138: 40.283 distance: 137 - 140: 36.707 distance: 138 - 139: 60.586 distance: 138 - 147: 41.087 distance: 139 - 194: 30.302 distance: 140 - 141: 33.378 distance: 141 - 142: 21.219 distance: 141 - 143: 39.365 distance: 142 - 144: 59.754 distance: 143 - 145: 40.416 distance: 145 - 146: 39.780 distance: 147 - 148: 51.174 distance: 148 - 149: 52.216 distance: 148 - 151: 33.190 distance: 149 - 150: 25.056 distance: 149 - 155: 28.801 distance: 151 - 153: 38.150 distance: 152 - 154: 57.540