Starting phenix.real_space_refine on Sun Mar 17 22:23:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/03_2024/6ifz_9659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/03_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_9659/03_2024/6ifz_9659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/03_2024/6ifz_9659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/03_2024/6ifz_9659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifz_9659/03_2024/6ifz_9659.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.39, per 1000 atoms: 0.49 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: 7.72 Conformation dependent library (CDL) restraints added in 3.0 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: 7.09 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: 6.23 Time building geometry restraints manager: 8.29 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 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.660 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 57.740 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.220 ------------------------------------------------------------------------------- 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 : 1.663 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: 0.3461 time to fit residues: 271.6216 Evaluate side-chains 305 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 295 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 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 A 175 ASN A 312 ASN A 436 HIS A 497 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2465 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= 0.185 Angle : 0.667 11.224 26829 Z= 0.350 Chirality : 0.043 0.347 3029 Planarity : 0.004 0.080 3226 Dihedral : 15.130 167.911 3404 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.22 % Favored : 91.64 % Rotamer: Outliers : 3.27 % Allowed : 17.62 % Favored : 79.11 % 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: -1.89 (0.16), residues: 764 sheet: -2.98 (0.24), residues: 344 loop : -3.07 (0.15), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 732 HIS 0.004 0.001 HIS A 436 PHE 0.023 0.001 PHE C 51 TYR 0.019 0.001 TYR A 122 ARG 0.008 0.001 ARG G 136 *********************** 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 440 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 379 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7019 (pp20) cc_final: 0.6816 (pp20) REVERT: A 74 TYR cc_start: 0.6824 (t80) cc_final: 0.6619 (t80) REVERT: A 183 PHE cc_start: 0.6531 (m-80) cc_final: 0.6232 (m-80) REVERT: A 228 LEU cc_start: 0.7545 (mp) cc_final: 0.7312 (tp) REVERT: A 384 TYR cc_start: 0.6394 (t80) cc_final: 0.5974 (t80) REVERT: A 388 MET cc_start: 0.7465 (ttm) cc_final: 0.7258 (ttm) REVERT: A 426 TYR cc_start: 0.7177 (t80) cc_final: 0.6938 (t80) REVERT: A 527 PHE cc_start: 0.6689 (t80) cc_final: 0.5399 (m-10) REVERT: A 728 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8020 (tp) REVERT: D 7 GLU cc_start: 0.7555 (pm20) cc_final: 0.7303 (pm20) REVERT: D 44 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8514 (tp) REVERT: C 84 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8359 (ttpt) REVERT: G 124 ASN cc_start: 0.8642 (p0) cc_final: 0.8247 (p0) REVERT: G 171 ARG cc_start: 0.6688 (tmm-80) cc_final: 0.6463 (mmm160) REVERT: E 46 ILE cc_start: 0.8690 (tt) cc_final: 0.8375 (mm) REVERT: E 174 LEU cc_start: 0.8843 (mt) cc_final: 0.8564 (mp) REVERT: B 219 LEU cc_start: 0.8073 (tt) cc_final: 0.7721 (mt) REVERT: B 278 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7770 (ttm170) REVERT: H 158 ARG cc_start: 0.7392 (mpt180) cc_final: 0.6345 (ttt90) REVERT: H 164 LYS cc_start: 0.7676 (mttt) cc_final: 0.7306 (tppt) REVERT: H 221 SER cc_start: 0.7672 (p) cc_final: 0.7364 (m) outliers start: 61 outliers final: 29 residues processed: 417 average time/residue: 0.3076 time to fit residues: 195.1860 Evaluate side-chains 324 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 293 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 549 SER 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 107 ASP Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 131 VAL 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: 9.9990 chunk 63 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 497 ASN G 137 GLN E 11 GLN E 144 ASN 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19674 Z= 0.289 Angle : 0.684 12.747 26829 Z= 0.355 Chirality : 0.045 0.351 3029 Planarity : 0.004 0.062 3226 Dihedral : 14.817 169.996 3393 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.06 % Favored : 89.85 % Rotamer: Outliers : 3.96 % Allowed : 20.46 % Favored : 75.58 % 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: -3.52 (0.16), residues: 2226 helix: -1.37 (0.17), residues: 783 sheet: -2.81 (0.25), residues: 353 loop : -2.92 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 732 HIS 0.005 0.001 HIS A 484 PHE 0.020 0.002 PHE G 167 TYR 0.018 0.002 TYR D 9 ARG 0.005 0.000 ARG G 128 *********************** 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 388 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 314 time to evaluate : 2.051 Fit side-chains REVERT: A 37 ASP cc_start: 0.7048 (m-30) cc_final: 0.6736 (t0) REVERT: A 183 PHE cc_start: 0.6696 (m-80) cc_final: 0.6284 (m-80) REVERT: A 384 TYR cc_start: 0.6504 (t80) cc_final: 0.6009 (t80) REVERT: A 388 MET cc_start: 0.7459 (ttm) cc_final: 0.7249 (ttm) REVERT: A 527 PHE cc_start: 0.5895 (t80) cc_final: 0.5429 (m-10) REVERT: A 728 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8164 (tp) REVERT: D 7 GLU cc_start: 0.7625 (pm20) cc_final: 0.7298 (pm20) REVERT: D 44 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8531 (tp) REVERT: C 46 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8933 (mt) REVERT: C 84 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8460 (ttpt) REVERT: G 124 ASN cc_start: 0.8775 (p0) cc_final: 0.8413 (p0) REVERT: G 171 ARG cc_start: 0.6779 (tmm-80) cc_final: 0.6363 (mmm160) REVERT: G 172 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5942 (m-30) REVERT: B 219 LEU cc_start: 0.8253 (tt) cc_final: 0.7962 (mt) REVERT: H 158 ARG cc_start: 0.7630 (mpt180) cc_final: 0.6550 (ttp-170) REVERT: H 164 LYS cc_start: 0.7834 (mttt) cc_final: 0.7445 (tppt) outliers start: 74 outliers final: 50 residues processed: 365 average time/residue: 0.3194 time to fit residues: 176.6055 Evaluate side-chains 335 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 281 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 545 SER 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 44 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 172 ASP 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 80 SER 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 F residue 177 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 24 LYS 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 246 HIS Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 155 ASP 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 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 59 optimal weight: 0.0010 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 497 ASN D 72 GLN G 85 ASN F 11 GLN E 11 GLN E 144 ASN 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19674 Z= 0.300 Angle : 0.672 12.749 26829 Z= 0.350 Chirality : 0.045 0.346 3029 Planarity : 0.004 0.059 3226 Dihedral : 14.765 169.861 3393 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.20 % Favored : 89.71 % Rotamer: Outliers : 4.71 % Allowed : 20.78 % Favored : 74.50 % 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: -3.23 (0.16), residues: 2226 helix: -1.06 (0.18), residues: 774 sheet: -2.69 (0.25), residues: 353 loop : -2.78 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 732 HIS 0.005 0.001 HIS A 484 PHE 0.019 0.002 PHE G 167 TYR 0.038 0.002 TYR A 74 ARG 0.005 0.000 ARG G 136 *********************** 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 400 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 312 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6913 (m-30) cc_final: 0.6621 (t0) REVERT: A 183 PHE cc_start: 0.6652 (m-80) cc_final: 0.6142 (m-80) REVERT: A 527 PHE cc_start: 0.5836 (t80) cc_final: 0.5301 (m-10) REVERT: D 7 GLU cc_start: 0.7733 (pm20) cc_final: 0.7451 (pm20) REVERT: D 44 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8528 (tt) REVERT: C 46 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8986 (mt) REVERT: G 124 ASN cc_start: 0.8784 (p0) cc_final: 0.8508 (p0) REVERT: G 148 ASP cc_start: 0.7504 (t70) cc_final: 0.7287 (p0) REVERT: G 168 LYS cc_start: 0.7159 (mmmt) cc_final: 0.6730 (tttt) REVERT: G 171 ARG cc_start: 0.6888 (tmm-80) cc_final: 0.6488 (mmm160) REVERT: F 89 LYS cc_start: 0.7849 (tppp) cc_final: 0.7488 (mtpt) REVERT: F 123 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: B 78 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6957 (t80) REVERT: B 219 LEU cc_start: 0.8261 (tt) cc_final: 0.7914 (mt) REVERT: H 158 ARG cc_start: 0.7420 (mpt180) cc_final: 0.6471 (ttp-170) REVERT: H 164 LYS cc_start: 0.7816 (mttt) cc_final: 0.7405 (tppt) outliers start: 88 outliers final: 59 residues processed: 375 average time/residue: 0.3219 time to fit residues: 182.7291 Evaluate side-chains 354 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 291 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 545 SER 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 752 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 46 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 11 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR 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 51 SER Chi-restraints excluded: chain F residue 123 GLU 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 F residue 177 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR 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 155 ASP 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: 0.8980 chunk 124 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 163 optimal weight: 0.0570 chunk 90 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN D 72 GLN G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19674 Z= 0.190 Angle : 0.613 11.780 26829 Z= 0.318 Chirality : 0.042 0.327 3029 Planarity : 0.003 0.057 3226 Dihedral : 14.641 170.457 3393 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.42 % Rotamer: Outliers : 4.02 % Allowed : 22.12 % Favored : 73.86 % 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: -2.97 (0.17), residues: 2226 helix: -0.73 (0.18), residues: 786 sheet: -2.43 (0.26), residues: 336 loop : -2.79 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 732 HIS 0.005 0.001 HIS A 484 PHE 0.030 0.001 PHE B 64 TYR 0.026 0.001 TYR A 74 ARG 0.005 0.000 ARG G 136 *********************** 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 403 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 328 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6800 (m-30) cc_final: 0.6573 (t0) REVERT: A 183 PHE cc_start: 0.6539 (m-80) cc_final: 0.6005 (m-80) REVERT: A 527 PHE cc_start: 0.5944 (t80) cc_final: 0.5434 (m-80) REVERT: C 15 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8116 (mtmm) REVERT: C 38 SER cc_start: 0.8902 (m) cc_final: 0.8530 (t) REVERT: G 124 ASN cc_start: 0.8648 (p0) cc_final: 0.8368 (p0) REVERT: G 148 ASP cc_start: 0.7465 (t70) cc_final: 0.7210 (p0) REVERT: G 164 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: G 171 ARG cc_start: 0.6652 (tmm-80) cc_final: 0.6415 (mmm160) REVERT: F 89 LYS cc_start: 0.7812 (tppp) cc_final: 0.7459 (mtpt) REVERT: F 123 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: B 219 LEU cc_start: 0.8169 (tt) cc_final: 0.7875 (mt) REVERT: H 158 ARG cc_start: 0.7395 (mpt180) cc_final: 0.6500 (ttt-90) REVERT: H 164 LYS cc_start: 0.7624 (mttt) cc_final: 0.7309 (tppt) outliers start: 75 outliers final: 51 residues processed: 383 average time/residue: 0.2669 time to fit residues: 154.7662 Evaluate side-chains 342 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 289 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 657 ARG Chi-restraints excluded: chain A residue 696 ASP 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 C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 107 ASP 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 42 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 123 GLU 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 12 ILE Chi-restraints excluded: chain E residue 24 ASP 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 197 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 55 GLN 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 H residue 75 LEU 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 Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 0.0670 chunk 197 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 219 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 D 72 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 ASN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3728 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= 0.145 Angle : 0.575 12.394 26829 Z= 0.298 Chirality : 0.041 0.330 3029 Planarity : 0.003 0.060 3226 Dihedral : 14.429 169.775 3391 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 3.91 % Allowed : 23.30 % Favored : 72.79 % 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: -2.68 (0.17), residues: 2226 helix: -0.48 (0.18), residues: 795 sheet: -2.28 (0.26), residues: 344 loop : -2.64 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 732 HIS 0.004 0.001 HIS A 484 PHE 0.032 0.001 PHE A 548 TYR 0.027 0.001 TYR C 59 ARG 0.005 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 422 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 349 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8787 (tp) cc_final: 0.8557 (tt) REVERT: A 351 LYS cc_start: 0.7367 (mmpt) cc_final: 0.6491 (tptt) REVERT: A 363 TYR cc_start: 0.7278 (t80) cc_final: 0.7026 (t80) REVERT: A 527 PHE cc_start: 0.5694 (t80) cc_final: 0.5469 (m-80) REVERT: A 622 ILE cc_start: 0.8461 (mp) cc_final: 0.8107 (mt) REVERT: G 148 ASP cc_start: 0.7448 (t70) cc_final: 0.7186 (p0) REVERT: G 164 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: G 171 ARG cc_start: 0.6566 (tmm-80) cc_final: 0.6267 (mmm160) REVERT: F 2 THR cc_start: 0.7192 (t) cc_final: 0.6892 (p) REVERT: F 123 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: F 190 TYR cc_start: 0.8404 (m-10) cc_final: 0.8065 (m-10) REVERT: E 162 GLN cc_start: 0.8058 (pt0) cc_final: 0.7823 (pt0) REVERT: B 78 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6576 (t80) REVERT: B 219 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7838 (mt) REVERT: H 158 ARG cc_start: 0.7328 (mpt180) cc_final: 0.6508 (ttt-90) outliers start: 73 outliers final: 48 residues processed: 397 average time/residue: 0.3234 time to fit residues: 194.2216 Evaluate side-chains 357 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 305 time to evaluate : 2.086 ------------------------------------------------------------------------------- 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 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP 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 C residue 36 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain E residue 12 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 197 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 LEU 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 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 0.3980 chunk 160 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 218 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 D 72 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19674 Z= 0.167 Angle : 0.589 13.456 26829 Z= 0.305 Chirality : 0.042 0.323 3029 Planarity : 0.003 0.055 3226 Dihedral : 14.374 170.301 3389 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.09 % Rotamer: Outliers : 3.91 % Allowed : 23.73 % Favored : 72.36 % 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: -2.47 (0.17), residues: 2226 helix: -0.27 (0.18), residues: 795 sheet: -2.17 (0.26), residues: 348 loop : -2.55 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 732 HIS 0.004 0.001 HIS A 484 PHE 0.044 0.001 PHE A 548 TYR 0.023 0.001 TYR A 300 ARG 0.006 0.000 ARG G 115 *********************** 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 391 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 318 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: A 351 LYS cc_start: 0.7382 (mmpt) cc_final: 0.6489 (tptt) REVERT: A 622 ILE cc_start: 0.8454 (mp) cc_final: 0.8141 (mt) REVERT: G 148 ASP cc_start: 0.7461 (t70) cc_final: 0.7199 (p0) REVERT: G 164 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: G 171 ARG cc_start: 0.6577 (tmm-80) cc_final: 0.6241 (mmm160) REVERT: G 172 ASP cc_start: 0.6282 (m-30) cc_final: 0.6011 (m-30) REVERT: F 2 THR cc_start: 0.7200 (t) cc_final: 0.6942 (p) REVERT: F 105 ASN cc_start: 0.8626 (p0) cc_final: 0.8221 (p0) REVERT: F 190 TYR cc_start: 0.8448 (m-10) cc_final: 0.8138 (m-10) REVERT: E 171 ARG cc_start: 0.7026 (ttp-110) cc_final: 0.6782 (mtp-110) REVERT: B 34 SER cc_start: 0.7709 (t) cc_final: 0.7271 (m) REVERT: B 78 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6704 (t80) REVERT: B 219 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7872 (mt) outliers start: 73 outliers final: 56 residues processed: 366 average time/residue: 0.3099 time to fit residues: 171.4819 Evaluate side-chains 359 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 299 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 549 SER Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP 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 74 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU 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 118 THR Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 LEU 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 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN C 23 ASN C 26 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19674 Z= 0.158 Angle : 0.583 13.803 26829 Z= 0.300 Chirality : 0.041 0.320 3029 Planarity : 0.003 0.053 3226 Dihedral : 14.322 170.442 3389 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.77 % Favored : 92.14 % Rotamer: Outliers : 3.75 % Allowed : 24.05 % Favored : 72.20 % 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: -0.14 (0.18), residues: 803 sheet: -2.00 (0.27), residues: 344 loop : -2.50 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 38 HIS 0.006 0.001 HIS A 55 PHE 0.060 0.001 PHE A 548 TYR 0.023 0.001 TYR D 68 ARG 0.006 0.000 ARG G 115 *********************** 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 398 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 328 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: A 351 LYS cc_start: 0.7334 (mmpt) cc_final: 0.6460 (tptt) REVERT: A 622 ILE cc_start: 0.8264 (mp) cc_final: 0.8014 (mt) REVERT: G 148 ASP cc_start: 0.7445 (t70) cc_final: 0.7181 (p0) REVERT: G 164 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: G 171 ARG cc_start: 0.6459 (tmm-80) cc_final: 0.6213 (mmm160) REVERT: G 172 ASP cc_start: 0.6343 (m-30) cc_final: 0.6051 (m-30) REVERT: F 2 THR cc_start: 0.7232 (t) cc_final: 0.6900 (p) REVERT: F 105 ASN cc_start: 0.8560 (p0) cc_final: 0.8246 (p0) REVERT: F 171 ARG cc_start: 0.7571 (tpt170) cc_final: 0.7368 (tpp-160) REVERT: E 64 TYR cc_start: 0.7903 (m-10) cc_final: 0.7515 (m-10) REVERT: E 171 ARG cc_start: 0.7158 (ttp-110) cc_final: 0.6946 (mtp-110) REVERT: B 34 SER cc_start: 0.7693 (t) cc_final: 0.7252 (m) REVERT: B 219 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7869 (mt) outliers start: 70 outliers final: 57 residues processed: 372 average time/residue: 0.3204 time to fit residues: 180.8622 Evaluate side-chains 365 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 305 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 202 SER 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 600 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP 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 74 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR 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 118 THR Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain E residue 12 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 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 131 VAL 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 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 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: 0.7795 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19674 Z= 0.201 Angle : 0.609 13.208 26829 Z= 0.314 Chirality : 0.042 0.317 3029 Planarity : 0.003 0.053 3226 Dihedral : 14.311 170.782 3385 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.72 % Favored : 91.19 % Rotamer: Outliers : 3.59 % Allowed : 24.58 % Favored : 71.83 % 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: -2.22 (0.17), residues: 2226 helix: -0.11 (0.18), residues: 798 sheet: -1.82 (0.28), residues: 332 loop : -2.45 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 38 HIS 0.010 0.001 HIS A 484 PHE 0.026 0.001 PHE A 183 TYR 0.022 0.001 TYR D 68 ARG 0.007 0.000 ARG G 115 *********************** 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 378 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 311 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.7344 (mmpt) cc_final: 0.6502 (tptt) REVERT: G 148 ASP cc_start: 0.7492 (t70) cc_final: 0.7252 (p0) REVERT: G 164 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: G 172 ASP cc_start: 0.6479 (m-30) cc_final: 0.6131 (m-30) REVERT: E 171 ARG cc_start: 0.7188 (ttp-110) cc_final: 0.6985 (mtp-110) REVERT: B 34 SER cc_start: 0.7687 (t) cc_final: 0.7265 (m) REVERT: B 78 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6773 (t80) REVERT: B 219 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7885 (mt) outliers start: 67 outliers final: 56 residues processed: 354 average time/residue: 0.3121 time to fit residues: 168.0677 Evaluate side-chains 358 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 299 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 202 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP 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 5 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR 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 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain E residue 12 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 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 78 TYR 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 165 LEU 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 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** 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: 0.7784 moved from start: 0.4147 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= 0.190 Angle : 0.611 14.712 26829 Z= 0.314 Chirality : 0.042 0.320 3029 Planarity : 0.003 0.053 3226 Dihedral : 14.306 170.496 3385 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.13 % Favored : 91.78 % Rotamer: Outliers : 3.43 % Allowed : 25.01 % Favored : 71.56 % 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: -2.18 (0.17), residues: 2226 helix: -0.09 (0.18), residues: 805 sheet: -1.73 (0.29), residues: 332 loop : -2.45 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 38 HIS 0.009 0.001 HIS A 484 PHE 0.027 0.001 PHE A 183 TYR 0.022 0.001 TYR D 68 ARG 0.008 0.000 ARG A 512 ********************** 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 372 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 308 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: A 351 LYS cc_start: 0.7351 (mmpt) cc_final: 0.6517 (tptt) REVERT: D 100 LYS cc_start: 0.7567 (pttp) cc_final: 0.7307 (pttm) REVERT: G 148 ASP cc_start: 0.7489 (t70) cc_final: 0.7241 (p0) REVERT: E 171 ARG cc_start: 0.7097 (ttp-110) cc_final: 0.6842 (mtp-110) REVERT: B 34 SER cc_start: 0.7707 (t) cc_final: 0.7266 (m) REVERT: B 78 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6780 (t80) REVERT: B 219 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7877 (mt) REVERT: H 53 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.6306 (mttp) outliers start: 64 outliers final: 56 residues processed: 348 average time/residue: 0.3180 time to fit residues: 166.8663 Evaluate side-chains 356 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 296 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 202 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP 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 C residue 5 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR 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 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain E residue 12 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 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 78 TYR 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 165 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 C 72 GLN C 76 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122340 restraints weight = 32169.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123338 restraints weight = 28076.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124991 restraints weight = 22074.011| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19674 Z= 0.201 Angle : 0.620 14.746 26829 Z= 0.318 Chirality : 0.042 0.319 3029 Planarity : 0.003 0.052 3226 Dihedral : 14.294 170.511 3385 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.54 % Favored : 91.37 % Rotamer: Outliers : 3.43 % Allowed : 24.96 % Favored : 71.61 % 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: -2.12 (0.17), residues: 2226 helix: -0.04 (0.18), residues: 794 sheet: -1.70 (0.29), residues: 332 loop : -2.39 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 38 HIS 0.009 0.001 HIS A 484 PHE 0.026 0.001 PHE A 183 TYR 0.023 0.001 TYR D 68 ARG 0.007 0.000 ARG A 512 =============================================================================== Job complete usr+sys time: 4002.08 seconds wall clock time: 75 minutes 17.69 seconds (4517.69 seconds total)