Starting phenix.real_space_refine on Wed Jun 25 00:34:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tas_41141/06_2025/8tas_41141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tas_41141/06_2025/8tas_41141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tas_41141/06_2025/8tas_41141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tas_41141/06_2025/8tas_41141.map" model { file = "/net/cci-nas-00/data/ceres_data/8tas_41141/06_2025/8tas_41141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tas_41141/06_2025/8tas_41141.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 386 5.49 5 S 118 5.16 5 C 17318 2.51 5 N 5401 2.21 5 O 6217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29440 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3633 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Chain: "E" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4580 Classifications: {'peptide': 570} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 538} Chain breaks: 4 Chain: "G" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2930 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "H" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3972 Classifications: {'DNA': 193} Link IDs: {'rna3p': 192} Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3919 Classifications: {'DNA': 193} Link IDs: {'rna3p': 192} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "W" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "X" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 666 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3139 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Chain: "Y" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1047 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 16.82, per 1000 atoms: 0.57 Number of scatterers: 29440 At special positions: 0 Unit cell: (165.564, 199.29, 168.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 P 386 15.00 O 6217 8.00 N 5401 7.00 C 17318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 571 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 578 " distance=2.03 Simple disulfide: pdb=" SG CYS E 571 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 590 " - pdb=" SG CYS E 593 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 3.3 seconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5102 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 32 sheets defined 37.8% alpha, 15.8% beta 120 base pairs and 281 stacking pairs defined. Time for finding SS restraints: 13.05 Creating SS restraints... Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 90 through 107 removed outlier: 3.507A pdb=" N ILE D 106 " --> pdb=" O THR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 removed outlier: 6.102A pdb=" N THR D 116 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR D 117 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 4.261A pdb=" N MET D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.661A pdb=" N MET D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 471 Processing helix chain 'D' and resid 502 through 508 removed outlier: 4.347A pdb=" N ILE D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS D 507 " --> pdb=" O PRO D 503 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 508' Processing helix chain 'D' and resid 539 through 543 Processing helix chain 'D' and resid 575 through 579 removed outlier: 3.553A pdb=" N MET D 579 " --> pdb=" O PRO D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 603 removed outlier: 3.962A pdb=" N ARG D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE D 603 " --> pdb=" O GLN D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 625 removed outlier: 3.845A pdb=" N VAL D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET D 614 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP D 617 " --> pdb=" O VAL D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 651 removed outlier: 3.778A pdb=" N MET D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET D 637 " --> pdb=" O ASN D 633 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS D 646 " --> pdb=" O ASN D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 Processing helix chain 'D' and resid 670 through 682 removed outlier: 3.952A pdb=" N ILE D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 678 " --> pdb=" O ILE D 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 63 removed outlier: 4.409A pdb=" N LYS E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU E 59 " --> pdb=" O ILE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 180 removed outlier: 3.996A pdb=" N PHE E 171 " --> pdb=" O ASN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.366A pdb=" N MET E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.582A pdb=" N LYS E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.918A pdb=" N SER E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 344 removed outlier: 3.616A pdb=" N ALA E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 453 removed outlier: 3.502A pdb=" N ILE E 449 " --> pdb=" O PHE E 445 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR E 451 " --> pdb=" O VAL E 447 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR E 452 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 removed outlier: 3.591A pdb=" N ILE E 459 " --> pdb=" O ASN E 455 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 460 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG E 461 " --> pdb=" O CYS E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 482 Processing helix chain 'E' and resid 500 through 515 removed outlier: 3.574A pdb=" N TRP E 504 " --> pdb=" O LYS E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 576 through 581 Processing helix chain 'E' and resid 609 through 614 Processing helix chain 'E' and resid 652 through 666 Processing helix chain 'E' and resid 687 through 692 removed outlier: 3.521A pdb=" N ARG E 690 " --> pdb=" O ASN E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 742 Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 267 through 280 removed outlier: 3.636A pdb=" N MET G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN G 272 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 removed outlier: 3.532A pdb=" N LEU I 48 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG I 53 " --> pdb=" O ARG I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 4.468A pdb=" N PHE I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN I 68 " --> pdb=" O LYS I 64 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.521A pdb=" N VAL I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 removed outlier: 3.548A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN I 125 " --> pdb=" O PRO I 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG I 131 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 30 through 41 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.571A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR J 71 " --> pdb=" O ARG J 67 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR J 72 " --> pdb=" O ASP J 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 93 removed outlier: 4.506A pdb=" N ALA J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 21 Processing helix chain 'R' and resid 26 through 36 Processing helix chain 'R' and resid 46 through 73 removed outlier: 3.806A pdb=" N TYR R 50 " --> pdb=" O GLY R 46 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN R 68 " --> pdb=" O GLU R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 removed outlier: 3.512A pdb=" N ARG R 88 " --> pdb=" O GLN R 84 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 89 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 95 removed outlier: 3.958A pdb=" N LYS R 95 " --> pdb=" O GLU R 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 46 removed outlier: 3.527A pdb=" N LYS S 43 " --> pdb=" O TYR S 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN S 44 " --> pdb=" O LYS S 40 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 81 removed outlier: 4.353A pdb=" N MET S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN S 64 " --> pdb=" O ASN S 60 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU S 73 " --> pdb=" O ARG S 69 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG S 76 " --> pdb=" O GLY S 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS S 79 " --> pdb=" O SER S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 99 removed outlier: 3.534A pdb=" N ILE S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG S 96 " --> pdb=" O GLN S 92 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU S 99 " --> pdb=" O VAL S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 121 removed outlier: 4.121A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS S 106 " --> pdb=" O GLU S 102 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER S 109 " --> pdb=" O LYS S 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 37 removed outlier: 3.787A pdb=" N VAL U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG U 35 " --> pdb=" O HIS U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 72 removed outlier: 3.610A pdb=" N ILE U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU U 63 " --> pdb=" O THR U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 89 removed outlier: 3.975A pdb=" N LEU U 85 " --> pdb=" O ARG U 81 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA U 86 " --> pdb=" O HIS U 82 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 95 removed outlier: 3.858A pdb=" N LYS U 95 " --> pdb=" O GLU U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 116 Processing helix chain 'V' and resid 34 through 44 removed outlier: 3.778A pdb=" N TYR V 39 " --> pdb=" O ALA V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 81 removed outlier: 4.479A pdb=" N MET V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN V 64 " --> pdb=" O ASN V 60 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU V 73 " --> pdb=" O ARG V 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU V 77 " --> pdb=" O GLU V 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA V 78 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 99 removed outlier: 4.119A pdb=" N ALA V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG V 96 " --> pdb=" O GLN V 92 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU V 97 " --> pdb=" O THR V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 121 removed outlier: 3.573A pdb=" N VAL V 108 " --> pdb=" O ALA V 104 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER V 109 " --> pdb=" O LYS V 105 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA V 114 " --> pdb=" O GLU V 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 55 removed outlier: 3.635A pdb=" N GLN W 55 " --> pdb=" O ILE W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 76 removed outlier: 3.614A pdb=" N GLU W 73 " --> pdb=" O ARG W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 114 removed outlier: 4.047A pdb=" N MET W 90 " --> pdb=" O SER W 86 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU W 92 " --> pdb=" O ALA W 88 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN W 93 " --> pdb=" O VAL W 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA W 95 " --> pdb=" O ALA W 91 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA W 102 " --> pdb=" O ALA W 98 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP W 106 " --> pdb=" O ALA W 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU W 109 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS W 110 " --> pdb=" O ASP W 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 132 removed outlier: 3.695A pdb=" N ILE W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN W 125 " --> pdb=" O PRO W 121 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU W 126 " --> pdb=" O LYS W 122 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG W 131 " --> pdb=" O ALA W 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 29 removed outlier: 3.841A pdb=" N ILE X 29 " --> pdb=" O ILE X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 42 removed outlier: 3.818A pdb=" N LEU X 37 " --> pdb=" O ALA X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 76 removed outlier: 3.893A pdb=" N GLY X 56 " --> pdb=" O GLU X 52 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR X 71 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 93 removed outlier: 4.214A pdb=" N TYR X 88 " --> pdb=" O MET X 84 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG X 92 " --> pdb=" O TYR X 88 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 28 removed outlier: 3.560A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 210 No H-bonds generated for 'chain 'O' and resid 208 through 210' Processing helix chain 'O' and resid 348 through 350 No H-bonds generated for 'chain 'O' and resid 348 through 350' Processing helix chain 'O' and resid 355 through 360 Processing helix chain 'O' and resid 406 through 410 removed outlier: 3.698A pdb=" N ASN O 410 " --> pdb=" O ASN O 407 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 210 removed outlier: 3.674A pdb=" N LEU Y 195 " --> pdb=" O ASP Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 259 No H-bonds generated for 'chain 'Y' and resid 257 through 259' Processing helix chain 'Y' and resid 270 through 272 No H-bonds generated for 'chain 'Y' and resid 270 through 272' Processing helix chain 'Y' and resid 275 through 281 removed outlier: 3.628A pdb=" N LEU Y 279 " --> pdb=" O ASP Y 275 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP Y 281 " --> pdb=" O ALA Y 277 " (cutoff:3.500A) Processing helix chain 'Y' and resid 282 through 285 Processing sheet with id=AA1, first strand: chain 'D' and resid 162 through 165 removed outlier: 4.688A pdb=" N GLY D 163 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN D 356 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE Y 227 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL Y 226 " --> pdb=" O HIS Y 242 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS Y 242 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA Y 228 " --> pdb=" O LEU Y 240 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Y 252 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.690A pdb=" N LEU D 159 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR D 358 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE Y 227 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 203 through 211 removed outlier: 3.619A pdb=" N THR D 208 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 186 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS D 210 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU D 184 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 438 through 443 removed outlier: 3.641A pdb=" N THR D 438 " --> pdb=" O TYR D 434 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE D 429 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL D 489 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN D 431 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE D 491 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU D 433 " --> pdb=" O ILE D 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 557 through 560 removed outlier: 4.114A pdb=" N LEU D 529 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL O 35 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN O 403 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE O 398 " --> pdb=" O SER O 394 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP O 402 " --> pdb=" O ILE O 390 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET O 404 " --> pdb=" O TRP O 388 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TRP O 388 " --> pdb=" O MET O 404 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL O 389 " --> pdb=" O ASN O 383 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN O 383 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP O 379 " --> pdb=" O VAL O 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.566A pdb=" N LEU D 572 " --> pdb=" O HIS D 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 94 through 97 removed outlier: 5.395A pdb=" N CYS G 84 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP G 438 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER G 433 " --> pdb=" O CYS G 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN G 415 " --> pdb=" O VAL G 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 removed outlier: 6.392A pdb=" N PHE E 120 " --> pdb=" O ILE E 650 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 285 through 286 Processing sheet with id=AB1, first strand: chain 'E' and resid 619 through 623 removed outlier: 4.134A pdb=" N ALA E 622 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 642 through 643 removed outlier: 4.470A pdb=" N ILE E 715 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 99 through 101 removed outlier: 4.617A pdb=" N GLN G 136 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU G 125 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU G 134 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 147 through 154 removed outlier: 3.968A pdb=" N ILE G 174 " --> pdb=" O LYS G 184 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS G 184 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 193 through 198 removed outlier: 6.111A pdb=" N VAL G 209 " --> pdb=" O ASN G 194 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU G 196 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU G 207 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE G 198 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU G 205 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER G 210 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA G 214 " --> pdb=" O SER G 210 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU G 215 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE G 228 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU G 217 " --> pdb=" O VAL G 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 239 through 244 Processing sheet with id=AB7, first strand: chain 'G' and resid 309 through 315 Processing sheet with id=AB8, first strand: chain 'G' and resid 369 through 370 removed outlier: 4.219A pdb=" N SER G 369 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.184A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AC2, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.530A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.429A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'U' and resid 42 through 43 removed outlier: 6.918A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AC7, first strand: chain 'W' and resid 83 through 84 removed outlier: 7.249A pdb=" N ARG W 83 " --> pdb=" O VAL X 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'O' and resid 47 through 49 removed outlier: 3.979A pdb=" N ASN O 77 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER O 83 " --> pdb=" O ILE O 117 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE O 117 " --> pdb=" O SER O 83 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLN O 85 " --> pdb=" O ILE O 115 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE O 115 " --> pdb=" O GLN O 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 129 through 133 removed outlier: 3.737A pdb=" N ARG O 129 " --> pdb=" O LYS O 143 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE O 139 " --> pdb=" O MET O 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 172 through 173 removed outlier: 6.397A pdb=" N ARG O 172 " --> pdb=" O VAL O 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'O' and resid 183 through 185 removed outlier: 3.554A pdb=" N LEU O 193 " --> pdb=" O TRP O 205 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP O 205 " --> pdb=" O LEU O 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 230 through 235 removed outlier: 4.342A pdb=" N ALA O 247 " --> pdb=" O LYS O 251 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS O 251 " --> pdb=" O ALA O 247 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 280 through 281 removed outlier: 3.539A pdb=" N SER O 280 " --> pdb=" O ALA O 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS O 311 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 320 through 325 removed outlier: 3.821A pdb=" N GLN O 322 " --> pdb=" O SER O 336 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER O 336 " --> pdb=" O GLN O 322 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN O 324 " --> pdb=" O ALA O 334 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA O 334 " --> pdb=" O GLN O 324 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP O 346 " --> pdb=" O LEU O 366 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU O 366 " --> pdb=" O ASP O 346 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 281 stacking parallelities Total time for adding SS restraints: 14.94 Time building geometry restraints manager: 8.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8435 1.34 - 1.46: 9127 1.46 - 1.59: 12354 1.59 - 1.71: 765 1.71 - 1.84: 171 Bond restraints: 30852 Sorted by residual: bond pdb=" C LEU S 99 " pdb=" N PRO S 100 " ideal model delta sigma weight residual 1.335 1.296 0.039 8.70e-03 1.32e+04 1.96e+01 bond pdb=" C2 SAH E 801 " pdb=" N3 SAH E 801 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C8 SAH E 801 " pdb=" N7 SAH E 801 " ideal model delta sigma weight residual 1.299 1.353 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" C2 SAH E 801 " pdb=" N1 SAH E 801 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" CA LEU J 97 " pdb=" CB LEU J 97 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.70e-02 3.46e+03 6.06e+00 ... (remaining 30847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 42609 3.97 - 7.94: 160 7.94 - 11.92: 519 11.92 - 15.89: 38 15.89 - 19.86: 14 Bond angle restraints: 43340 Sorted by residual: angle pdb=" O3' DC T 67 " pdb=" P DC T 68 " pdb=" OP1 DC T 68 " ideal model delta sigma weight residual 108.00 127.86 -19.86 3.00e+00 1.11e-01 4.38e+01 angle pdb=" O3' DG T 46 " pdb=" P DA T 47 " pdb=" OP1 DA T 47 " ideal model delta sigma weight residual 108.00 127.03 -19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" O3' DC T 150 " pdb=" P DC T 151 " pdb=" OP1 DC T 151 " ideal model delta sigma weight residual 108.00 126.96 -18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" O3' DC H 104 " pdb=" P DG H 105 " pdb=" OP1 DG H 105 " ideal model delta sigma weight residual 108.00 126.69 -18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" O3' DC T 120 " pdb=" P DC T 121 " pdb=" OP1 DC T 121 " ideal model delta sigma weight residual 108.00 126.50 -18.50 3.00e+00 1.11e-01 3.80e+01 ... (remaining 43335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15859 35.89 - 71.78: 1643 71.78 - 107.67: 61 107.67 - 143.56: 3 143.56 - 179.45: 24 Dihedral angle restraints: 17590 sinusoidal: 9746 harmonic: 7844 Sorted by residual: dihedral pdb=" CB CYS E 565 " pdb=" SG CYS E 565 " pdb=" SG CYS E 578 " pdb=" CB CYS E 578 " ideal model delta sinusoidal sigma weight residual -86.00 -174.31 88.31 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS E 565 " pdb=" SG CYS E 565 " pdb=" SG CYS E 571 " pdb=" CB CYS E 571 " ideal model delta sinusoidal sigma weight residual -86.00 -165.38 79.38 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS E 590 " pdb=" SG CYS E 590 " pdb=" SG CYS E 593 " pdb=" CB CYS E 593 " ideal model delta sinusoidal sigma weight residual 93.00 150.00 -57.00 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 17587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 4459 0.124 - 0.247: 37 0.247 - 0.371: 103 0.371 - 0.495: 184 0.495 - 0.618: 21 Chirality restraints: 4804 Sorted by residual: chirality pdb=" P DC T 68 " pdb=" OP1 DC T 68 " pdb=" OP2 DC T 68 " pdb=" O5' DC T 68 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" P DC T 110 " pdb=" OP1 DC T 110 " pdb=" OP2 DC T 110 " pdb=" O5' DC T 110 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" P DC T 151 " pdb=" OP1 DC T 151 " pdb=" OP2 DC T 151 " pdb=" O5' DC T 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.75e+00 ... (remaining 4801 not shown) Planarity restraints: 4208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 326 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO E 327 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO E 327 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 327 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 80 " -0.036 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR V 80 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR V 80 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR V 80 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR V 80 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR V 80 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR V 80 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR V 80 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 67 " -0.014 2.00e-02 2.50e+03 1.51e-02 3.99e+00 pdb=" CG PHE I 67 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 67 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE I 67 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE I 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE I 67 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 67 " -0.001 2.00e-02 2.50e+03 ... (remaining 4205 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 713 2.63 - 3.20: 28738 3.20 - 3.77: 53240 3.77 - 4.33: 70130 4.33 - 4.90: 101065 Nonbonded interactions: 253886 Sorted by model distance: nonbonded pdb=" OH TYR J 98 " pdb=" OD2 ASP S 65 " model vdw 2.069 3.040 nonbonded pdb=" O CYS E 567 " pdb=" OG1 THR E 592 " model vdw 2.098 3.040 nonbonded pdb=" OD2 ASP O 318 " pdb=" OG1 THR O 338 " model vdw 2.104 3.040 nonbonded pdb=" OG SER G 210 " pdb=" OD1 ASP G 212 " model vdw 2.110 3.040 nonbonded pdb=" O HIS V 106 " pdb=" OG SER V 109 " model vdw 2.124 3.040 ... (remaining 253881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and resid 37 through 135) selection = chain 'W' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'X' and resid 20 through 102) } ncs_group { reference = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) selection = chain 'U' } ncs_group { reference = (chain 'S' and resid 28 through 122) selection = chain 'V' } 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 77.020 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 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 : 0.006 0.095 30856 Z= 0.258 Angle : 1.417 19.860 43348 Z= 0.567 Chirality : 0.108 0.618 4804 Planarity : 0.005 0.128 4208 Dihedral : 23.568 179.445 12476 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2632 helix: -1.00 (0.17), residues: 870 sheet: -0.73 (0.26), residues: 385 loop : -1.10 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 113 HIS 0.008 0.001 HIS X 75 PHE 0.035 0.002 PHE I 67 TYR 0.058 0.002 TYR V 80 ARG 0.005 0.001 ARG U 77 Details of bonding type rmsd hydrogen bonds : bond 0.30886 ( 1071) hydrogen bonds : angle 10.94658 ( 2756) SS BOND : bond 0.00752 ( 4) SS BOND : angle 3.21059 ( 8) covalent geometry : bond 0.00573 (30852) covalent geometry : angle 1.41666 (43340) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.781 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: J 84 MET cc_start: 0.7819 (mmm) cc_final: 0.6985 (mpp) REVERT: R 38 ASN cc_start: 0.8261 (m-40) cc_final: 0.7991 (m-40) REVERT: X 49 LEU cc_start: 0.8762 (tp) cc_final: 0.8562 (tp) REVERT: O 36 MET cc_start: 0.0594 (tpt) cc_final: -0.0227 (tpt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.4035 time to fit residues: 74.3134 Evaluate side-chains 87 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 50.0000 chunk 226 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 chunk 77 optimal weight: 0.0000 chunk 152 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 234 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 271 optimal weight: 9.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 HIS D 166 HIS D 356 GLN D 449 HIS D 517 ASN D 624 HIS D 667 ASN E 45 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 273 GLN E 331 GLN E 520 ASN G 146 ASN G 160 HIS ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 ASN G 283 ASN G 382 GLN I 108 ASN S 92 GLN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN V 46 HIS V 92 GLN W 39 HIS W 125 GLN ** O 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 ASN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.108823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.093971 restraints weight = 160657.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093805 restraints weight = 288927.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.093178 restraints weight = 220004.430| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30856 Z= 0.166 Angle : 0.660 8.517 43348 Z= 0.371 Chirality : 0.043 0.248 4804 Planarity : 0.005 0.124 4208 Dihedral : 28.200 178.326 7122 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2632 helix: -0.11 (0.17), residues: 907 sheet: -1.10 (0.25), residues: 397 loop : -0.95 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 255 HIS 0.005 0.001 HIS X 75 PHE 0.018 0.001 PHE O 243 TYR 0.021 0.002 TYR V 80 ARG 0.009 0.000 ARG J 39 Details of bonding type rmsd hydrogen bonds : bond 0.08979 ( 1071) hydrogen bonds : angle 5.50614 ( 2756) SS BOND : bond 0.01702 ( 4) SS BOND : angle 2.54065 ( 8) covalent geometry : bond 0.00362 (30852) covalent geometry : angle 0.65885 (43340) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 2.685 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: J 84 MET cc_start: 0.7699 (mmm) cc_final: 0.7274 (mpp) REVERT: S 92 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6567 (tp40) REVERT: U 78 ILE cc_start: 0.8127 (mt) cc_final: 0.7924 (mt) REVERT: V 56 MET cc_start: 0.8338 (tpt) cc_final: 0.7639 (tmm) REVERT: V 65 ASP cc_start: 0.8406 (t0) cc_final: 0.8101 (t0) REVERT: V 80 TYR cc_start: 0.8367 (m-10) cc_final: 0.8073 (m-80) REVERT: X 49 LEU cc_start: 0.8481 (tp) cc_final: 0.8266 (tp) outliers start: 4 outliers final: 0 residues processed: 124 average time/residue: 0.3907 time to fit residues: 81.0091 Evaluate side-chains 92 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 60 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 271 optimal weight: 50.0000 chunk 182 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN J 75 HIS R 31 HIS S 92 GLN S 106 HIS V 81 ASN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 410 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.108047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093033 restraints weight = 160943.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.092496 restraints weight = 318941.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.092516 restraints weight = 245476.370| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 30856 Z= 0.168 Angle : 0.612 8.088 43348 Z= 0.340 Chirality : 0.041 0.236 4804 Planarity : 0.004 0.121 4208 Dihedral : 28.065 179.217 7122 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.97 (0.16), residues: 2632 helix: 0.06 (0.17), residues: 905 sheet: -1.11 (0.24), residues: 393 loop : -0.91 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 255 HIS 0.013 0.001 HIS D 659 PHE 0.015 0.001 PHE O 243 TYR 0.015 0.001 TYR V 80 ARG 0.004 0.000 ARG R 71 Details of bonding type rmsd hydrogen bonds : bond 0.07871 ( 1071) hydrogen bonds : angle 5.11102 ( 2756) SS BOND : bond 0.00670 ( 4) SS BOND : angle 2.36513 ( 8) covalent geometry : bond 0.00375 (30852) covalent geometry : angle 0.61123 (43340) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 4.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.7188 (tmm) cc_final: 0.6912 (tmm) REVERT: V 65 ASP cc_start: 0.8351 (t0) cc_final: 0.7974 (t0) REVERT: V 80 TYR cc_start: 0.8310 (m-10) cc_final: 0.7920 (m-10) REVERT: X 49 LEU cc_start: 0.8560 (tp) cc_final: 0.8177 (tp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4215 time to fit residues: 82.9712 Evaluate side-chains 90 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 231 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 238 optimal weight: 0.7980 chunk 264 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 overall best weight: 7.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN E 273 GLN E 279 HIS ** E 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 81 ASN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN X 25 ASN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.101161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.088625 restraints weight = 167694.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.087645 restraints weight = 309827.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.086551 restraints weight = 283300.258| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.169 30856 Z= 0.734 Angle : 1.151 18.124 43348 Z= 0.617 Chirality : 0.065 0.399 4804 Planarity : 0.009 0.121 4208 Dihedral : 29.225 175.510 7122 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 36.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.24 % Favored : 91.60 % Rotamer: Outliers : 0.55 % Allowed : 6.89 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.06 (0.16), residues: 2632 helix: -1.36 (0.16), residues: 900 sheet: -1.00 (0.25), residues: 381 loop : -1.40 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 113 HIS 0.024 0.003 HIS X 75 PHE 0.063 0.003 PHE I 67 TYR 0.049 0.004 TYR W 54 ARG 0.012 0.001 ARG J 67 Details of bonding type rmsd hydrogen bonds : bond 0.12030 ( 1071) hydrogen bonds : angle 6.86725 ( 2756) SS BOND : bond 0.02457 ( 4) SS BOND : angle 5.76553 ( 8) covalent geometry : bond 0.01679 (30852) covalent geometry : angle 1.14888 (43340) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 39 TYR cc_start: 0.7741 (t80) cc_final: 0.7478 (t80) REVERT: S 56 MET cc_start: 0.8633 (tmm) cc_final: 0.8042 (tmm) REVERT: V 56 MET cc_start: 0.9084 (tpp) cc_final: 0.8750 (tpp) REVERT: X 49 LEU cc_start: 0.9052 (tp) cc_final: 0.8779 (tp) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.4239 time to fit residues: 74.2193 Evaluate side-chains 88 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 213 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 248 optimal weight: 50.0000 chunk 294 optimal weight: 0.2980 chunk 283 optimal weight: 50.0000 chunk 293 optimal weight: 8.9990 chunk 263 optimal weight: 50.0000 chunk 169 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 262 optimal weight: 50.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 567 HIS E 273 GLN E 575 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 HIS ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN R 38 ASN S 92 GLN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 HIS ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.106906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.092188 restraints weight = 162104.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.091866 restraints weight = 336854.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.092027 restraints weight = 265991.067| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 30856 Z= 0.172 Angle : 0.667 8.813 43348 Z= 0.368 Chirality : 0.043 0.272 4804 Planarity : 0.005 0.120 4208 Dihedral : 28.869 179.595 7122 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2632 helix: -0.37 (0.17), residues: 912 sheet: -1.19 (0.24), residues: 400 loop : -1.09 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 255 HIS 0.015 0.001 HIS G 213 PHE 0.023 0.002 PHE E 456 TYR 0.020 0.002 TYR G 124 ARG 0.010 0.001 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.07798 ( 1071) hydrogen bonds : angle 5.13958 ( 2756) SS BOND : bond 0.01114 ( 4) SS BOND : angle 3.71488 ( 8) covalent geometry : bond 0.00384 (30852) covalent geometry : angle 0.66489 (43340) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.7196 (tmm) cc_final: 0.6918 (tmm) REVERT: J 84 MET cc_start: 0.7350 (mmm) cc_final: 0.6884 (mpp) REVERT: R 50 TYR cc_start: 0.7376 (t80) cc_final: 0.7127 (t80) REVERT: R 84 GLN cc_start: 0.8545 (tp40) cc_final: 0.8331 (tp-100) REVERT: S 56 MET cc_start: 0.8082 (tmm) cc_final: 0.7726 (tmm) REVERT: V 39 TYR cc_start: 0.8292 (t80) cc_final: 0.7976 (t80) REVERT: V 56 MET cc_start: 0.8821 (tpp) cc_final: 0.8617 (tpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4899 time to fit residues: 95.1088 Evaluate side-chains 93 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 236 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 219 optimal weight: 0.2980 chunk 156 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 81 ASN S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 68 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 272 HIS ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.104630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.091123 restraints weight = 163808.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.091120 restraints weight = 352633.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.090920 restraints weight = 267754.170| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 30856 Z= 0.292 Angle : 0.725 9.152 43348 Z= 0.396 Chirality : 0.045 0.250 4804 Planarity : 0.005 0.122 4208 Dihedral : 28.821 176.478 7122 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2632 helix: -0.55 (0.17), residues: 910 sheet: -1.06 (0.25), residues: 392 loop : -1.16 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 113 HIS 0.013 0.001 HIS D 659 PHE 0.018 0.002 PHE E 729 TYR 0.020 0.002 TYR J 72 ARG 0.009 0.001 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.07863 ( 1071) hydrogen bonds : angle 5.41711 ( 2756) SS BOND : bond 0.00915 ( 4) SS BOND : angle 3.73243 ( 8) covalent geometry : bond 0.00672 (30852) covalent geometry : angle 0.72313 (43340) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 180 MET cc_start: 0.6820 (mmm) cc_final: 0.6620 (mmm) REVERT: S 56 MET cc_start: 0.8431 (tmm) cc_final: 0.7747 (tmm) REVERT: V 56 MET cc_start: 0.8934 (tpp) cc_final: 0.8493 (tpp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.4948 time to fit residues: 85.8687 Evaluate side-chains 88 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 244 optimal weight: 0.5980 chunk 24 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 chunk 241 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 607 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 400 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.105736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.093106 restraints weight = 161564.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.092922 restraints weight = 327454.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.092554 restraints weight = 235052.140| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30856 Z= 0.206 Angle : 0.664 8.591 43348 Z= 0.364 Chirality : 0.042 0.219 4804 Planarity : 0.005 0.121 4208 Dihedral : 28.764 179.211 7122 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2632 helix: -0.35 (0.17), residues: 921 sheet: -1.05 (0.25), residues: 395 loop : -1.11 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 255 HIS 0.014 0.001 HIS D 659 PHE 0.025 0.001 PHE I 67 TYR 0.013 0.001 TYR J 72 ARG 0.007 0.000 ARG X 55 Details of bonding type rmsd hydrogen bonds : bond 0.07403 ( 1071) hydrogen bonds : angle 5.10824 ( 2756) SS BOND : bond 0.00369 ( 4) SS BOND : angle 3.94147 ( 8) covalent geometry : bond 0.00470 (30852) covalent geometry : angle 0.66196 (43340) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 84 MET cc_start: 0.7493 (mmm) cc_final: 0.6954 (mpp) REVERT: S 39 TYR cc_start: 0.8048 (t80) cc_final: 0.7797 (t80) REVERT: S 56 MET cc_start: 0.8171 (tmm) cc_final: 0.7742 (tmm) REVERT: V 56 MET cc_start: 0.8891 (tpp) cc_final: 0.8540 (tpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.4537 time to fit residues: 77.3852 Evaluate side-chains 90 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 140 optimal weight: 0.2980 chunk 81 optimal weight: 0.0000 chunk 193 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 297 optimal weight: 50.0000 chunk 232 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 222 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 273 GLN E 331 GLN E 575 GLN ** E 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN S 92 GLN W 68 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.107503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.094602 restraints weight = 162904.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.094206 restraints weight = 310106.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.093935 restraints weight = 228654.571| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30856 Z= 0.146 Angle : 0.619 10.823 43348 Z= 0.340 Chirality : 0.040 0.207 4804 Planarity : 0.004 0.121 4208 Dihedral : 28.500 179.850 7122 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 0.09 % Allowed : 1.36 % Favored : 98.55 % 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: -0.94 (0.16), residues: 2632 helix: 0.13 (0.17), residues: 902 sheet: -0.90 (0.25), residues: 383 loop : -1.00 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 255 HIS 0.011 0.001 HIS D 659 PHE 0.014 0.001 PHE G 296 TYR 0.015 0.001 TYR S 80 ARG 0.010 0.000 ARG E 712 Details of bonding type rmsd hydrogen bonds : bond 0.07406 ( 1071) hydrogen bonds : angle 4.69757 ( 2756) SS BOND : bond 0.00638 ( 4) SS BOND : angle 3.11185 ( 8) covalent geometry : bond 0.00325 (30852) covalent geometry : angle 0.61761 (43340) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 3.003 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: D 299 MET cc_start: 0.5405 (ppp) cc_final: 0.5073 (tpt) REVERT: J 84 MET cc_start: 0.7760 (mmm) cc_final: 0.7247 (mpp) REVERT: V 56 MET cc_start: 0.8763 (tpp) cc_final: 0.8482 (tpp) REVERT: V 65 ASP cc_start: 0.8408 (t0) cc_final: 0.8073 (t0) outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.4539 time to fit residues: 84.3911 Evaluate side-chains 94 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 179 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 290 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 242 optimal weight: 0.0870 chunk 291 optimal weight: 50.0000 chunk 215 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.107125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.094398 restraints weight = 162328.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.093977 restraints weight = 313425.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.093489 restraints weight = 250364.642| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 30856 Z= 0.152 Angle : 0.611 10.197 43348 Z= 0.335 Chirality : 0.040 0.211 4804 Planarity : 0.004 0.120 4208 Dihedral : 28.402 179.269 7122 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -0.85 (0.16), residues: 2632 helix: 0.23 (0.17), residues: 898 sheet: -0.84 (0.25), residues: 383 loop : -0.97 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 255 HIS 0.012 0.001 HIS D 659 PHE 0.022 0.001 PHE U 25 TYR 0.013 0.001 TYR J 72 ARG 0.008 0.000 ARG E 461 Details of bonding type rmsd hydrogen bonds : bond 0.07185 ( 1071) hydrogen bonds : angle 4.69116 ( 2756) SS BOND : bond 0.00479 ( 4) SS BOND : angle 2.66676 ( 8) covalent geometry : bond 0.00343 (30852) covalent geometry : angle 0.60987 (43340) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 2.637 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: D 637 MET cc_start: 0.7320 (mmp) cc_final: 0.7100 (mmp) REVERT: J 84 MET cc_start: 0.7735 (mmm) cc_final: 0.7145 (mpp) REVERT: U 78 ILE cc_start: 0.8327 (mt) cc_final: 0.8115 (mt) REVERT: V 56 MET cc_start: 0.8793 (tpp) cc_final: 0.8420 (tpp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.4246 time to fit residues: 73.8859 Evaluate side-chains 90 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 19 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 471 HIS ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 68 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.106225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.093559 restraints weight = 164077.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.093329 restraints weight = 321394.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.092917 restraints weight = 226027.848| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 30856 Z= 0.189 Angle : 0.637 10.460 43348 Z= 0.348 Chirality : 0.041 0.224 4804 Planarity : 0.005 0.121 4208 Dihedral : 28.442 177.716 7122 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.47 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.91 (0.16), residues: 2632 helix: 0.12 (0.17), residues: 905 sheet: -0.89 (0.25), residues: 393 loop : -0.96 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 113 HIS 0.012 0.001 HIS D 659 PHE 0.019 0.001 PHE U 25 TYR 0.016 0.001 TYR J 72 ARG 0.007 0.000 ARG J 92 Details of bonding type rmsd hydrogen bonds : bond 0.07122 ( 1071) hydrogen bonds : angle 4.82267 ( 2756) SS BOND : bond 0.00512 ( 4) SS BOND : angle 2.78527 ( 8) covalent geometry : bond 0.00432 (30852) covalent geometry : angle 0.63630 (43340) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.646 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: D 637 MET cc_start: 0.7177 (mmp) cc_final: 0.6829 (mmp) REVERT: V 56 MET cc_start: 0.8867 (tpp) cc_final: 0.8395 (tpp) REVERT: V 80 TYR cc_start: 0.8551 (m-10) cc_final: 0.7616 (m-10) REVERT: O 404 MET cc_start: 0.3473 (mpp) cc_final: 0.3100 (mpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.4557 time to fit residues: 75.5733 Evaluate side-chains 88 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 23 optimal weight: 30.0000 chunk 231 optimal weight: 4.9990 chunk 121 optimal weight: 0.0570 chunk 178 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN W 68 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.107510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.094456 restraints weight = 163502.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.094067 restraints weight = 310646.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.093733 restraints weight = 231244.960| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30856 Z= 0.145 Angle : 0.608 10.458 43348 Z= 0.333 Chirality : 0.040 0.222 4804 Planarity : 0.004 0.120 4208 Dihedral : 28.348 179.653 7122 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.72 (0.16), residues: 2632 helix: 0.37 (0.17), residues: 897 sheet: -0.84 (0.25), residues: 382 loop : -0.89 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 255 HIS 0.012 0.001 HIS D 659 PHE 0.016 0.001 PHE U 25 TYR 0.013 0.001 TYR W 41 ARG 0.009 0.000 ARG J 92 Details of bonding type rmsd hydrogen bonds : bond 0.07272 ( 1071) hydrogen bonds : angle 4.56496 ( 2756) SS BOND : bond 0.00579 ( 4) SS BOND : angle 2.63681 ( 8) covalent geometry : bond 0.00327 (30852) covalent geometry : angle 0.60738 (43340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6741.33 seconds wall clock time: 121 minutes 9.89 seconds (7269.89 seconds total)