Starting phenix.real_space_refine on Wed Aug 7 04:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/08_2024/6ifz_9659.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/08_2024/6ifz_9659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/08_2024/6ifz_9659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/08_2024/6ifz_9659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/08_2024/6ifz_9659.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/08_2024/6ifz_9659.cif" } resolution = 3.58 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 ------------------------------------------------------------------------------- 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= 0.012 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 62 5.49 5 S 37 5.16 5 C 12029 2.51 5 N 3257 2.21 5 O 3799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19185 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5799 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 8, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1697 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1623 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2319 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2750 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 606 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2935 SG CYS A 404 55.785 30.462 65.300 1.00 51.21 S ATOM 3079 SG CYS A 422 58.862 33.242 65.609 1.00 46.39 S Time building chain proxies: 10.49, per 1000 atoms: 0.55 Number of scatterers: 19185 At special positions: 0 Unit cell: (93.6, 135.2, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 37 16.00 P 62 15.00 O 3799 8.00 N 3257 7.00 C 12029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.71 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 422 " 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 37.2% alpha, 11.2% beta 21 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 5.96 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.805A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.832A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.341A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.639A pdb=" N THR A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.856A pdb=" N TYR A 141 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 159 removed outlier: 4.048A pdb=" N ARG A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.821A pdb=" N ASN A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 4.041A pdb=" N PHE A 183 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 197 through 219 removed outlier: 4.958A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.682A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 266 through 291 removed outlier: 3.964A pdb=" N ARG A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 335 removed outlier: 3.690A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 378 removed outlier: 4.213A pdb=" N TYR A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLN A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.824A pdb=" N ASN A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.608A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 4.022A pdb=" N SER A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.684A pdb=" N LYS A 503 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 529 removed outlier: 3.776A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.219A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.586A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.609A pdb=" N ILE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.978A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.773A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.795A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'D' and resid 8 through 18 removed outlier: 3.652A pdb=" N ALA D 16 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 57 removed outlier: 3.569A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 78 removed outlier: 4.029A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.111A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.626A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 4.166A pdb=" N ARG D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 Processing helix chain 'C' and resid 37 through 55 removed outlier: 4.749A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 64 through 78 removed outlier: 3.765A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'G' and resid 48 through 62 removed outlier: 3.542A pdb=" N LEU G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 177 removed outlier: 3.742A pdb=" N ASP G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE G 167 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.669A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 83 removed outlier: 3.527A pdb=" N SER F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.634A pdb=" N PHE F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.523A pdb=" N GLY F 189 " --> pdb=" O GLY F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.550A pdb=" N THR F 211 " --> pdb=" O ASP F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 212 through 217 removed outlier: 3.867A pdb=" N LEU F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.873A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 162 through 165 Processing helix chain 'E' and resid 166 through 178 removed outlier: 4.171A pdb=" N ASP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.804A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 110 through 118 removed outlier: 4.024A pdb=" N LEU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.540A pdb=" N GLY B 185 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.649A pdb=" N ASP B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.582A pdb=" N LEU H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.591A pdb=" N LEU H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 148 removed outlier: 4.065A pdb=" N ASN H 148 " --> pdb=" O PRO H 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 145 through 148' Processing helix chain 'H' and resid 236 through 245 removed outlier: 3.663A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 4.558A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.418A pdb=" N GLN A 107 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.517A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 569 through 574 removed outlier: 4.754A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 612 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 96 through 97 Processing sheet with id=AA7, first strand: chain 'G' and resid 102 through 103 removed outlier: 4.161A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 118 through 122 Processing sheet with id=AA9, first strand: chain 'F' and resid 146 through 149 Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 149 removed outlier: 7.037A pdb=" N LYS F 5 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR F 202 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS F 7 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA F 200 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.301A pdb=" N SER E 9 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU E 198 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.748A pdb=" N LEU E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 123 Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.020A pdb=" N PHE B 64 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 160 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS B 4 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB9, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AC1, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.512A pdb=" N TYR B 143 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AC3, first strand: chain 'H' and resid 227 through 230 Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AC5, first strand: chain 'H' and resid 203 through 206 598 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3478 1.32 - 1.45: 5330 1.45 - 1.57: 10677 1.57 - 1.69: 123 1.69 - 1.82: 66 Bond restraints: 19674 Sorted by residual: bond pdb=" C GLN H 275 " pdb=" N TYR H 276 " ideal model delta sigma weight residual 1.331 1.422 -0.091 2.07e-02 2.33e+03 1.95e+01 bond pdb=" N TYR G 181 " pdb=" CA TYR G 181 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.32e-02 5.74e+03 9.20e+00 bond pdb=" N LEU A 160 " pdb=" CA LEU A 160 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.07e+00 bond pdb=" CA ARG H 158 " pdb=" C ARG H 158 " ideal model delta sigma weight residual 1.523 1.562 -0.040 1.41e-02 5.03e+03 7.89e+00 bond pdb=" N ILE E 29 " pdb=" CA ILE E 29 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.47e+00 ... (remaining 19669 not shown) Histogram of bond angle deviations from ideal: 95.21 - 103.20: 256 103.20 - 111.19: 7454 111.19 - 119.18: 8722 119.18 - 127.17: 10136 127.17 - 135.16: 261 Bond angle restraints: 26829 Sorted by residual: angle pdb=" N GLY H 314 " pdb=" CA GLY H 314 " pdb=" C GLY H 314 " ideal model delta sigma weight residual 112.73 127.67 -14.94 1.20e+00 6.94e-01 1.55e+02 angle pdb=" N SER H 107 " pdb=" CA SER H 107 " pdb=" C SER H 107 " ideal model delta sigma weight residual 112.45 95.21 17.24 1.39e+00 5.18e-01 1.54e+02 angle pdb=" N ARG F 95 " pdb=" CA ARG F 95 " pdb=" C ARG F 95 " ideal model delta sigma weight residual 112.24 126.42 -14.18 1.28e+00 6.10e-01 1.23e+02 angle pdb=" N ARG E 95 " pdb=" CA ARG E 95 " pdb=" C ARG E 95 " ideal model delta sigma weight residual 112.24 125.39 -13.15 1.28e+00 6.10e-01 1.06e+02 angle pdb=" N LYS H 161 " pdb=" CA LYS H 161 " pdb=" C LYS H 161 " ideal model delta sigma weight residual 110.23 121.06 -10.83 1.45e+00 4.76e-01 5.57e+01 ... (remaining 26824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 11448 34.04 - 68.07: 398 68.07 - 102.11: 33 102.11 - 136.15: 1 136.15 - 170.19: 3 Dihedral angle restraints: 11883 sinusoidal: 5288 harmonic: 6595 Sorted by residual: dihedral pdb=" CA TYR B 78 " pdb=" C TYR B 78 " pdb=" N PRO B 79 " pdb=" CA PRO B 79 " ideal model delta harmonic sigma weight residual 180.00 45.13 134.87 0 5.00e+00 4.00e-02 7.28e+02 dihedral pdb=" O4' C I 14 " pdb=" C1' C I 14 " pdb=" N1 C I 14 " pdb=" C2 C I 14 " ideal model delta sinusoidal sigma weight residual -128.00 42.19 -170.19 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C I 8 " pdb=" C1' C I 8 " pdb=" N1 C I 8 " pdb=" C2 C I 8 " ideal model delta sinusoidal sigma weight residual -128.00 34.41 -162.41 1 1.70e+01 3.46e-03 6.49e+01 ... (remaining 11880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2849 0.119 - 0.239: 159 0.239 - 0.358: 14 0.358 - 0.477: 4 0.477 - 0.596: 3 Chirality restraints: 3029 Sorted by residual: chirality pdb=" CA PHE H 159 " pdb=" N PHE H 159 " pdb=" C PHE H 159 " pdb=" CB PHE H 159 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CA ARG F 95 " pdb=" N ARG F 95 " pdb=" C ARG F 95 " pdb=" CB ARG F 95 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CA ARG E 95 " pdb=" N ARG E 95 " pdb=" C ARG E 95 " pdb=" CB ARG E 95 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 ... (remaining 3026 not shown) Planarity restraints: 3226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.066 2.00e-02 2.50e+03 2.89e-02 2.50e+01 pdb=" N9 G I 21 " -0.071 2.00e-02 2.50e+03 pdb=" C8 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G I 21 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.024 2.00e-02 2.50e+03 pdb=" N1 G I 21 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G I 21 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 638 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C GLY A 638 " -0.082 2.00e-02 2.50e+03 pdb=" O GLY A 638 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN A 639 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.055 2.00e-02 2.50e+03 2.62e-02 1.88e+01 pdb=" N9 A I 27 " -0.065 2.00e-02 2.50e+03 pdb=" C8 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.015 2.00e-02 2.50e+03 pdb=" N1 A I 27 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.005 2.00e-02 2.50e+03 ... (remaining 3223 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 9 1.99 - 2.71: 1309 2.71 - 3.44: 26631 3.44 - 4.17: 47514 4.17 - 4.90: 85260 Nonbonded interactions: 160723 Sorted by model distance: nonbonded pdb=" ND2 ASN A 639 " pdb=" OG SER A 643 " model vdw 1.258 3.120 nonbonded pdb=" CZ PHE H 260 " pdb=" NZ LYS H 313 " model vdw 1.364 3.420 nonbonded pdb=" CE1 PHE H 260 " pdb=" NZ LYS H 313 " model vdw 1.424 3.420 nonbonded pdb=" CD1 LEU H 225 " pdb=" CD2 LEU H 335 " model vdw 1.771 3.880 nonbonded pdb=" CD2 LEU C 46 " pdb=" O ALA G 25 " model vdw 1.838 3.460 ... (remaining 160718 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 'C' selection = (chain 'D' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 99 or (resid 100 and (name N or nam \ e CA or name C or name O or name CB )) or resid 101 through 123)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) selection = (chain 'F' and (resid 2 through 66 or resid 76 through 156 or (resid 157 through \ 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throu \ gh 217)) selection = (chain 'G' and (resid 2 through 66 or resid 76 through 158 or (resid 159 through \ 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throu \ gh 217)) } 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: 1.160 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 56.530 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.008 0.091 19674 Z= 0.537 Angle : 1.149 18.860 26829 Z= 0.656 Chirality : 0.067 0.596 3029 Planarity : 0.006 0.060 3226 Dihedral : 17.374 170.186 7629 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.69 % Favored : 88.81 % Rotamer: Outliers : 0.96 % Allowed : 10.93 % Favored : 88.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -5.16 (0.13), residues: 2226 helix: -3.36 (0.12), residues: 785 sheet: -3.36 (0.23), residues: 362 loop : -3.46 (0.14), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A 732 HIS 0.008 0.002 HIS A 695 PHE 0.045 0.003 PHE F 98 TYR 0.028 0.003 TYR D 9 ARG 0.017 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 523 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6308 (t60) cc_final: 0.6106 (t60) REVERT: A 170 ILE cc_start: 0.7013 (tp) cc_final: 0.6487 (tt) REVERT: A 183 PHE cc_start: 0.6605 (m-80) cc_final: 0.6283 (m-80) REVERT: A 228 LEU cc_start: 0.7736 (mp) cc_final: 0.7319 (tp) REVERT: A 384 TYR cc_start: 0.6242 (t80) cc_final: 0.6016 (t80) REVERT: A 527 PHE cc_start: 0.6481 (t80) cc_final: 0.5538 (m-10) REVERT: A 623 SER cc_start: 0.8495 (m) cc_final: 0.8259 (p) REVERT: A 641 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6453 (tttp) REVERT: D 22 ARG cc_start: 0.6446 (mpt-90) cc_final: 0.6192 (mpt-90) REVERT: D 44 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8691 (tp) REVERT: G 8 PHE cc_start: 0.7715 (m-80) cc_final: 0.7473 (m-80) REVERT: G 70 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6230 (tp30) REVERT: G 127 ASP cc_start: 0.7909 (t0) cc_final: 0.7682 (t0) REVERT: E 156 THR cc_start: 0.6417 (t) cc_final: 0.5931 (p) REVERT: B 219 LEU cc_start: 0.8059 (tt) cc_final: 0.7687 (tp) REVERT: B 278 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7891 (ttm170) REVERT: H 50 MET cc_start: 0.7759 (tmm) cc_final: 0.7547 (tmm) REVERT: H 158 ARG cc_start: 0.7564 (mpt180) cc_final: 0.6332 (ttp-170) REVERT: H 319 THR cc_start: 0.9284 (p) cc_final: 0.8498 (p) REVERT: H 345 MET cc_start: 0.8329 (tpt) cc_final: 0.7715 (tpt) outliers start: 18 outliers final: 8 residues processed: 539 average time/residue: 0.3455 time to fit residues: 271.7133 Evaluate side-chains 305 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 295 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain H residue 167 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 175 ASN A 312 ASN A 414 HIS A 436 HIS A 497 ASN A 676 HIS A 695 HIS A 699 ASN A 727 ASN D 72 GLN G 11 GLN G 159 ASN F 33 ASN F 213 ASN E 144 ASN B 11 GLN B 81 HIS B 135 GLN B 137 HIS B 144 GLN B 152 ASN B 174 GLN B 284 HIS H 22 ASN ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 275 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19674 Z= 0.190 Angle : 0.692 11.947 26829 Z= 0.365 Chirality : 0.044 0.386 3029 Planarity : 0.004 0.081 3226 Dihedral : 15.122 167.922 3404 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 2.68 % Allowed : 17.09 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.15), residues: 2226 helix: -1.91 (0.16), residues: 764 sheet: -3.04 (0.24), residues: 346 loop : -3.03 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 732 HIS 0.004 0.001 HIS A 55 PHE 0.023 0.001 PHE C 51 TYR 0.017 0.002 TYR A 122 ARG 0.007 0.001 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 387 time to evaluate : 2.146 Fit side-chains REVERT: A 183 PHE cc_start: 0.6549 (m-80) cc_final: 0.6219 (m-80) REVERT: A 228 LEU cc_start: 0.7526 (mp) cc_final: 0.7305 (tp) REVERT: A 351 LYS cc_start: 0.7273 (mmpt) cc_final: 0.6592 (tptt) REVERT: A 384 TYR cc_start: 0.6410 (t80) cc_final: 0.6056 (t80) REVERT: A 388 MET cc_start: 0.7474 (ttm) cc_final: 0.7236 (ttm) REVERT: A 426 TYR cc_start: 0.7203 (t80) cc_final: 0.6984 (t80) REVERT: A 527 PHE cc_start: 0.6688 (t80) cc_final: 0.5417 (m-10) REVERT: A 641 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6688 (tptt) REVERT: A 728 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8160 (tp) REVERT: D 7 GLU cc_start: 0.7461 (pm20) cc_final: 0.7227 (pm20) REVERT: D 44 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (tp) REVERT: G 64 TYR cc_start: 0.7480 (m-10) cc_final: 0.6985 (m-10) REVERT: G 124 ASN cc_start: 0.8574 (p0) cc_final: 0.8167 (p0) REVERT: G 171 ARG cc_start: 0.6654 (tmm-80) cc_final: 0.6401 (mmm160) REVERT: E 46 ILE cc_start: 0.8719 (tt) cc_final: 0.8452 (mm) REVERT: E 129 ILE cc_start: 0.7930 (mm) cc_final: 0.7711 (mm) REVERT: E 146 THR cc_start: 0.8039 (p) cc_final: 0.7760 (p) REVERT: E 171 ARG cc_start: 0.6931 (ttp-110) cc_final: 0.6728 (ttp-110) REVERT: E 174 LEU cc_start: 0.8820 (mt) cc_final: 0.8530 (mp) REVERT: B 219 LEU cc_start: 0.8016 (tt) cc_final: 0.7671 (mt) REVERT: B 278 ARG cc_start: 0.8144 (ttp-170) cc_final: 0.7715 (ttm170) REVERT: H 158 ARG cc_start: 0.7399 (mpt180) cc_final: 0.6353 (ttt90) REVERT: H 221 SER cc_start: 0.7715 (p) cc_final: 0.7436 (m) outliers start: 50 outliers final: 21 residues processed: 418 average time/residue: 0.3298 time to fit residues: 208.6718 Evaluate side-chains 317 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 293 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 497 ASN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN H 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19674 Z= 0.296 Angle : 0.700 12.851 26829 Z= 0.366 Chirality : 0.046 0.396 3029 Planarity : 0.004 0.062 3226 Dihedral : 14.867 172.587 3397 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.39 % Favored : 90.52 % Rotamer: Outliers : 3.54 % Allowed : 19.18 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.16), residues: 2226 helix: -1.40 (0.17), residues: 780 sheet: -2.86 (0.24), residues: 352 loop : -2.94 (0.16), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 732 HIS 0.005 0.001 HIS A 484 PHE 0.019 0.002 PHE G 167 TYR 0.035 0.002 TYR A 74 ARG 0.007 0.001 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 313 time to evaluate : 2.031 Fit side-chains REVERT: A 183 PHE cc_start: 0.6640 (m-80) cc_final: 0.6262 (m-80) REVERT: A 384 TYR cc_start: 0.6557 (t80) cc_final: 0.6071 (t80) REVERT: A 388 MET cc_start: 0.7450 (ttm) cc_final: 0.7229 (ttm) REVERT: A 527 PHE cc_start: 0.5814 (t80) cc_final: 0.5369 (m-10) REVERT: A 633 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: A 728 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8187 (tp) REVERT: D 7 GLU cc_start: 0.7601 (pm20) cc_final: 0.7269 (pm20) REVERT: D 44 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8487 (tp) REVERT: G 64 TYR cc_start: 0.7515 (m-10) cc_final: 0.7065 (m-10) REVERT: G 124 ASN cc_start: 0.8741 (p0) cc_final: 0.8415 (p0) REVERT: G 171 ARG cc_start: 0.6511 (tmm-80) cc_final: 0.6307 (mmm160) REVERT: F 79 LEU cc_start: 0.7744 (mp) cc_final: 0.7464 (tt) REVERT: F 172 ASP cc_start: 0.7009 (m-30) cc_final: 0.6683 (m-30) REVERT: E 150 GLU cc_start: 0.7526 (pm20) cc_final: 0.7283 (pm20) REVERT: B 5 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7930 (pp) REVERT: B 219 LEU cc_start: 0.8171 (tt) cc_final: 0.7869 (mt) REVERT: H 153 VAL cc_start: 0.6970 (t) cc_final: 0.6767 (t) REVERT: H 158 ARG cc_start: 0.7608 (mpt180) cc_final: 0.6547 (ttp-170) outliers start: 66 outliers final: 41 residues processed: 355 average time/residue: 0.3094 time to fit residues: 167.6306 Evaluate side-chains 324 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 279 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19674 Z= 0.193 Angle : 0.628 11.526 26829 Z= 0.328 Chirality : 0.043 0.370 3029 Planarity : 0.004 0.060 3226 Dihedral : 14.684 171.029 3393 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.27 % Favored : 91.64 % Rotamer: Outliers : 3.59 % Allowed : 20.03 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.16), residues: 2226 helix: -0.97 (0.18), residues: 792 sheet: -2.67 (0.25), residues: 344 loop : -2.79 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 732 HIS 0.004 0.001 HIS A 484 PHE 0.016 0.001 PHE A 548 TYR 0.028 0.001 TYR A 74 ARG 0.004 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 337 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6760 (m-30) cc_final: 0.6498 (t0) REVERT: A 183 PHE cc_start: 0.6685 (m-80) cc_final: 0.6145 (m-80) REVERT: A 351 LYS cc_start: 0.7354 (mmpt) cc_final: 0.6439 (tptt) REVERT: A 527 PHE cc_start: 0.5863 (t80) cc_final: 0.5315 (m-80) REVERT: A 728 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8275 (tp) REVERT: D 7 GLU cc_start: 0.7561 (pm20) cc_final: 0.7337 (pm20) REVERT: C 69 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9203 (mp) REVERT: G 64 TYR cc_start: 0.7444 (m-10) cc_final: 0.7006 (m-10) REVERT: G 124 ASN cc_start: 0.8531 (p0) cc_final: 0.8170 (p0) REVERT: G 164 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: G 172 ASP cc_start: 0.6338 (m-30) cc_final: 0.6054 (m-30) REVERT: F 89 LYS cc_start: 0.7783 (tppp) cc_final: 0.7451 (mtpt) REVERT: F 123 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: F 172 ASP cc_start: 0.6738 (m-30) cc_final: 0.6516 (m-30) REVERT: E 150 GLU cc_start: 0.7413 (pm20) cc_final: 0.7210 (pm20) REVERT: B 5 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7907 (pp) REVERT: B 219 LEU cc_start: 0.8096 (tt) cc_final: 0.7814 (mt) REVERT: H 43 MET cc_start: 0.8066 (mmm) cc_final: 0.7624 (mmt) REVERT: H 158 ARG cc_start: 0.7450 (mpt180) cc_final: 0.6528 (ttt-90) outliers start: 67 outliers final: 37 residues processed: 384 average time/residue: 0.3306 time to fit residues: 192.8857 Evaluate side-chains 336 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 294 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 0.0470 chunk 124 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19674 Z= 0.205 Angle : 0.624 12.058 26829 Z= 0.324 Chirality : 0.043 0.367 3029 Planarity : 0.003 0.059 3226 Dihedral : 14.570 171.518 3390 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.40 % Favored : 91.51 % Rotamer: Outliers : 4.07 % Allowed : 20.14 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.16), residues: 2226 helix: -0.73 (0.18), residues: 793 sheet: -2.50 (0.26), residues: 344 loop : -2.70 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 732 HIS 0.005 0.001 HIS A 484 PHE 0.028 0.001 PHE B 64 TYR 0.027 0.001 TYR A 74 ARG 0.006 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 313 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6800 (m-30) cc_final: 0.6530 (t0) REVERT: A 183 PHE cc_start: 0.6662 (m-80) cc_final: 0.6078 (m-80) REVERT: A 268 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: A 351 LYS cc_start: 0.7271 (mmpt) cc_final: 0.6439 (tptt) REVERT: A 527 PHE cc_start: 0.5836 (t80) cc_final: 0.5300 (m-80) REVERT: A 728 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8092 (tp) REVERT: D 7 GLU cc_start: 0.7481 (pm20) cc_final: 0.7251 (pm20) REVERT: D 85 ASP cc_start: 0.7491 (t0) cc_final: 0.7219 (t0) REVERT: C 15 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8094 (mtmm) REVERT: G 64 TYR cc_start: 0.7422 (m-10) cc_final: 0.6971 (m-10) REVERT: G 124 ASN cc_start: 0.8577 (p0) cc_final: 0.8222 (p0) REVERT: G 164 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: F 89 LYS cc_start: 0.7812 (tppp) cc_final: 0.7489 (mtpt) REVERT: B 219 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7825 (mt) REVERT: H 158 ARG cc_start: 0.7401 (mpt180) cc_final: 0.6469 (ttt-90) outliers start: 76 outliers final: 48 residues processed: 372 average time/residue: 0.3180 time to fit residues: 179.3654 Evaluate side-chains 345 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 293 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 19 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 0.0970 chunk 197 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 219 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN H 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19674 Z= 0.189 Angle : 0.615 12.628 26829 Z= 0.318 Chirality : 0.043 0.360 3029 Planarity : 0.003 0.058 3226 Dihedral : 14.473 171.600 3390 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 3.86 % Allowed : 21.21 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.17), residues: 2226 helix: -0.51 (0.18), residues: 790 sheet: -2.31 (0.27), residues: 334 loop : -2.59 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 732 HIS 0.004 0.001 HIS A 484 PHE 0.031 0.001 PHE A 548 TYR 0.023 0.001 TYR A 300 ARG 0.006 0.000 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 327 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6732 (m-30) cc_final: 0.6500 (t0) REVERT: A 268 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6615 (mp10) REVERT: A 351 LYS cc_start: 0.7436 (mmpt) cc_final: 0.6535 (tptt) REVERT: A 527 PHE cc_start: 0.5594 (t80) cc_final: 0.5376 (m-80) REVERT: A 622 ILE cc_start: 0.8580 (mp) cc_final: 0.8318 (mt) REVERT: A 728 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7895 (tp) REVERT: D 75 TYR cc_start: 0.8883 (t80) cc_final: 0.8632 (t80) REVERT: G 124 ASN cc_start: 0.8557 (p0) cc_final: 0.8228 (p0) REVERT: G 164 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: G 168 LYS cc_start: 0.7061 (mmmt) cc_final: 0.6503 (tppt) REVERT: E 150 GLU cc_start: 0.7378 (pm20) cc_final: 0.7170 (pm20) REVERT: B 219 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7840 (mt) REVERT: H 158 ARG cc_start: 0.7219 (mpt180) cc_final: 0.6446 (ttt-90) outliers start: 72 outliers final: 53 residues processed: 377 average time/residue: 0.3147 time to fit residues: 181.1368 Evaluate side-chains 360 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 303 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 19 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 229 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7495 > 50: distance: 44 - 49: 24.161 distance: 49 - 50: 14.199 distance: 50 - 51: 15.092 distance: 50 - 53: 7.013 distance: 51 - 52: 22.797 distance: 51 - 57: 32.593 distance: 53 - 54: 3.684 distance: 53 - 55: 17.136 distance: 54 - 56: 25.065 distance: 57 - 58: 20.853 distance: 58 - 59: 12.965 distance: 58 - 61: 20.895 distance: 59 - 60: 6.344 distance: 61 - 62: 28.297 distance: 61 - 63: 22.966 distance: 64 - 65: 28.640 distance: 65 - 66: 22.888 distance: 65 - 68: 12.546 distance: 66 - 67: 38.031 distance: 66 - 72: 12.701 distance: 68 - 69: 13.645 distance: 69 - 70: 12.952 distance: 69 - 71: 24.637 distance: 72 - 73: 4.222 distance: 73 - 74: 4.576 distance: 73 - 76: 22.718 distance: 74 - 75: 22.759 distance: 74 - 80: 49.757 distance: 76 - 77: 5.768 distance: 77 - 78: 23.001 distance: 77 - 79: 12.108 distance: 80 - 81: 20.559 distance: 80 - 86: 41.228 distance: 81 - 82: 22.846 distance: 81 - 84: 22.120 distance: 82 - 83: 24.976 distance: 82 - 87: 10.320 distance: 84 - 85: 42.798 distance: 85 - 86: 11.533 distance: 87 - 88: 11.013 distance: 88 - 89: 12.213 distance: 88 - 91: 6.279 distance: 89 - 90: 16.107 distance: 89 - 95: 16.056 distance: 91 - 92: 20.697 distance: 91 - 93: 12.102 distance: 92 - 94: 9.252 distance: 95 - 96: 24.885 distance: 96 - 97: 4.403 distance: 96 - 99: 24.753 distance: 97 - 98: 14.230 distance: 97 - 103: 9.378 distance: 99 - 100: 26.193 distance: 99 - 101: 15.551 distance: 100 - 102: 23.691 distance: 103 - 104: 30.545 distance: 103 - 109: 20.546 distance: 104 - 105: 22.961 distance: 104 - 107: 19.825 distance: 105 - 106: 15.194 distance: 105 - 110: 48.791 distance: 107 - 108: 32.947 distance: 108 - 109: 26.880 distance: 111 - 112: 17.061 distance: 112 - 113: 22.492 distance: 112 - 114: 13.663 distance: 113 - 134: 26.474 distance: 114 - 115: 7.822 distance: 115 - 116: 13.435 distance: 115 - 118: 6.795 distance: 116 - 117: 15.271 distance: 116 - 120: 7.331 distance: 117 - 139: 22.384 distance: 118 - 119: 9.991