Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:51:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/02_2023/6ifz_9659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/02_2023/6ifz_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_9659/02_2023/6ifz_9659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/02_2023/6ifz_9659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/02_2023/6ifz_9659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/02_2023/6ifz_9659.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 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-4877/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: 10.71, per 1000 atoms: 0.56 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: 7.52 Conformation dependent library (CDL) restraints added in 2.9 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: 5.29 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: 6.08 Time building geometry restraints manager: 8.03 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: 11340 34.04 - 68.07: 329 68.07 - 102.11: 20 102.11 - 136.15: 1 136.15 - 170.19: 3 Dihedral angle restraints: 11693 sinusoidal: 5098 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 11690 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 2.520 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 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 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. 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.480 Check model and map are aligned: 0.270 Process input model: 55.130 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 16.350 170.186 7439 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 % 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 *********************** 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 : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 539 average time/residue: 0.3582 time to fit residues: 281.6010 Evaluate side-chains 294 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 286 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1726 time to fit residues: 5.3787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN A 312 ASN A 329 GLN A 436 HIS A 497 ASN A 639 ASN A 676 HIS A 695 HIS A 699 ASN A 727 ASN D 72 GLN C 23 ASN C 26 ASN G 11 GLN G 85 ASN G 134 ASN G 159 ASN F 33 ASN F 213 ASN E 144 ASN B 11 GLN B 81 HIS B 116 ASN B 135 GLN B 137 HIS B 144 GLN B 152 ASN B 174 GLN B 284 HIS H 22 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 275 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 19674 Z= 0.188 Angle : 0.677 11.370 26829 Z= 0.355 Chirality : 0.044 0.353 3029 Planarity : 0.004 0.083 3226 Dihedral : 11.832 168.380 3194 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.54 % Favored : 91.33 % Rotamer Outliers : 2.79 % 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: -4.01 (0.15), residues: 2226 helix: -1.95 (0.16), residues: 763 sheet: -3.08 (0.24), residues: 356 loop : -3.05 (0.16), residues: 1107 *********************** 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 428 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 376 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 25 residues processed: 404 average time/residue: 0.3211 time to fit residues: 197.9213 Evaluate side-chains 317 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 2.168 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1807 time to fit residues: 11.4238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 19674 Z= 0.234 Angle : 0.651 12.205 26829 Z= 0.339 Chirality : 0.044 0.357 3029 Planarity : 0.004 0.061 3226 Dihedral : 11.435 169.222 3194 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.48 % Favored : 90.43 % Rotamer Outliers : 2.36 % 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: -3.50 (0.16), residues: 2226 helix: -1.36 (0.17), residues: 787 sheet: -2.82 (0.25), residues: 358 loop : -2.90 (0.16), residues: 1081 *********************** 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 371 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 327 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 357 average time/residue: 0.3328 time to fit residues: 179.8583 Evaluate side-chains 309 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 289 time to evaluate : 2.152 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2095 time to fit residues: 10.2346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 0.0370 chunk 155 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 138 optimal weight: 0.0050 chunk 207 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 59 optimal weight: 0.0000 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 ASN H 148 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 19674 Z= 0.137 Angle : 0.581 11.154 26829 Z= 0.302 Chirality : 0.041 0.331 3029 Planarity : 0.003 0.062 3226 Dihedral : 11.113 167.287 3194 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.05 % Favored : 92.86 % Rotamer Outliers : 1.98 % 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: -2.95 (0.16), residues: 2226 helix: -0.81 (0.18), residues: 794 sheet: -2.48 (0.26), residues: 344 loop : -2.68 (0.17), residues: 1088 *********************** 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 414 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 377 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 398 average time/residue: 0.3302 time to fit residues: 199.0933 Evaluate side-chains 328 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 312 time to evaluate : 2.141 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1871 time to fit residues: 8.4517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 5.9990 chunk 124 optimal weight: 0.0070 chunk 3 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 0.0030 chunk 187 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 699 ASN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 19674 Z= 0.180 Angle : 0.587 14.285 26829 Z= 0.305 Chirality : 0.042 0.311 3029 Planarity : 0.004 0.094 3226 Dihedral : 11.010 169.066 3194 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.27 % Favored : 91.64 % Rotamer Outliers : 2.04 % 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: -2.73 (0.17), residues: 2226 helix: -0.49 (0.18), residues: 796 sheet: -2.33 (0.26), residues: 356 loop : -2.69 (0.17), residues: 1074 *********************** 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 364 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 326 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 351 average time/residue: 0.3394 time to fit residues: 182.1262 Evaluate side-chains 319 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 302 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2187 time to fit residues: 9.5074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 0.5980 chunk 197 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 19674 Z= 0.262 Angle : 0.640 13.432 26829 Z= 0.331 Chirality : 0.044 0.315 3029 Planarity : 0.004 0.091 3226 Dihedral : 11.132 169.881 3194 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.93 % Rotamer Outliers : 2.04 % 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: -2.61 (0.17), residues: 2226 helix: -0.38 (0.18), residues: 786 sheet: -2.16 (0.26), residues: 351 loop : -2.64 (0.17), residues: 1089 *********************** 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 341 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 303 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 326 average time/residue: 0.3463 time to fit residues: 172.1841 Evaluate side-chains 309 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 291 time to evaluate : 1.956 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1733 time to fit residues: 8.6290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 218 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19674 Z= 0.241 Angle : 0.633 12.906 26829 Z= 0.327 Chirality : 0.043 0.333 3029 Planarity : 0.004 0.080 3226 Dihedral : 11.123 169.636 3194 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.93 % Rotamer Outliers : 1.45 % 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: -2.50 (0.17), residues: 2226 helix: -0.29 (0.19), residues: 788 sheet: -2.04 (0.27), residues: 349 loop : -2.61 (0.17), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 7 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 334 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 307 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 322 average time/residue: 0.3477 time to fit residues: 169.4894 Evaluate side-chains 295 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2029 time to fit residues: 8.3663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN D 72 GLN ** G 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 19674 Z= 0.447 Angle : 0.778 13.906 26829 Z= 0.399 Chirality : 0.049 0.367 3029 Planarity : 0.005 0.082 3226 Dihedral : 11.527 170.768 3194 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.87 % Favored : 89.04 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.05 % 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: -2.73 (0.17), residues: 2226 helix: -0.55 (0.18), residues: 780 sheet: -2.17 (0.27), residues: 349 loop : -2.68 (0.17), residues: 1097 *********************** REFINEMENT MACRO_CYCLE 8 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 340 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 301 time to evaluate : 2.136 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 27 residues processed: 322 average time/residue: 0.3323 time to fit residues: 162.4016 Evaluate side-chains 297 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 270 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1929 time to fit residues: 12.6433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 0.0770 chunk 191 optimal weight: 1.9990 chunk 203 optimal weight: 0.0060 chunk 122 optimal weight: 0.0010 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 497 ASN D 72 GLN C 23 ASN C 26 ASN G 137 GLN F 105 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19674 Z= 0.163 Angle : 0.632 11.290 26829 Z= 0.325 Chirality : 0.043 0.338 3029 Planarity : 0.004 0.076 3226 Dihedral : 11.112 170.274 3194 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.91 % Favored : 92.00 % Rotamer Outliers : 0.75 % 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: -2.41 (0.17), residues: 2226 helix: -0.21 (0.19), residues: 792 sheet: -1.99 (0.27), residues: 356 loop : -2.57 (0.17), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 9 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 334 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 320 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 331 average time/residue: 0.3267 time to fit residues: 166.0955 Evaluate side-chains 287 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 282 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2068 time to fit residues: 5.0948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 149 optimal weight: 0.0980 chunk 226 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 191 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN H 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 19674 Z= 0.162 Angle : 0.631 15.272 26829 Z= 0.320 Chirality : 0.042 0.323 3029 Planarity : 0.004 0.117 3226 Dihedral : 10.948 171.503 3194 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer Outliers : 0.32 % 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: -2.19 (0.17), residues: 2226 helix: -0.04 (0.19), residues: 794 sheet: -1.83 (0.28), residues: 346 loop : -2.45 (0.17), residues: 1086 ********************** REFINEMENT MACRO_CYCLE 10 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 321 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 315 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 317 average time/residue: 0.3252 time to fit residues: 158.1163 Evaluate side-chains 296 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1828 time to fit residues: 3.6614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 180 optimal weight: 0.4980 chunk 75 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN D 72 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 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 = 0.3701 r_free = 0.3701 target = 0.138532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118276 restraints weight = 32342.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119212 restraints weight = 27038.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120666 restraints weight = 21741.159| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4115 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= 0.322 Angle : 0.702 13.383 26829 Z= 0.360 Chirality : 0.046 0.355 3029 Planarity : 0.004 0.091 3226 Dihedral : 11.129 171.127 3194 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.88 % Favored : 90.03 % Rotamer Outliers : 0.64 % 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: -2.31 (0.17), residues: 2226 helix: -0.13 (0.18), residues: 785 sheet: -1.83 (0.28), residues: 345 loop : -2.54 (0.17), residues: 1096 =============================================================================== Job complete usr+sys time: 3931.70 seconds wall clock time: 72 minutes 17.80 seconds (4337.80 seconds total)