Starting phenix.real_space_refine (version: dev) on Thu Feb 23 04:43:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/02_2023/6ig0_9660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/02_2023/6ig0_9660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/02_2023/6ig0_9660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/02_2023/6ig0_9660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/02_2023/6ig0_9660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/02_2023/6ig0_9660_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 6": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H ARG 158": "NH1" <-> "NH2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19354 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5812 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 8, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 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: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2748 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 17, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 715 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 20, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 2, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2929 SG CYS A 401 57.965 30.672 66.675 1.00 74.37 S ATOM 2952 SG CYS A 404 55.630 31.804 64.016 1.00 70.96 S ATOM 3074 SG CYS A 419 58.898 30.714 62.945 1.00 75.02 S ATOM 3096 SG CYS A 422 58.767 34.241 63.931 1.00 70.14 S Time building chain proxies: 11.38, per 1000 atoms: 0.59 Number of scatterers: 19354 At special positions: 0 Unit cell: (92.56, 136.24, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 37 16.00 P 72 15.00 Mg 2 11.99 O 3856 8.00 N 3296 7.00 C 12090 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.71 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 422 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 419 " Number of angles added : 6 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4262 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 21 sheets defined 32.9% alpha, 8.1% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.610A pdb=" N TYR A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.750A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 removed outlier: 4.288A pdb=" N GLY A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.981A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.588A pdb=" N ILE A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.808A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.628A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 219 removed outlier: 3.540A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 266 through 290 removed outlier: 3.726A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.947A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.663A pdb=" N LEU A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.708A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 542 through 558 removed outlier: 3.625A pdb=" N PHE A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.791A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 3.633A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 666 through 675 removed outlier: 3.563A pdb=" N ASN A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.913A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 4.091A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 752 Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 37 through 51 removed outlier: 3.734A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 79 removed outlier: 4.190A pdb=" N ILE D 66 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 72 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D 73 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN D 76 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 79 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.630A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 102 through 121 Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 37 through 51 removed outlier: 3.733A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 62 through 79 removed outlier: 4.190A pdb=" N ILE C 66 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 72 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE C 73 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN C 76 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 79 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.629A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 102 through 121 Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.803A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 111 Processing helix chain 'G' and resid 162 through 179 removed outlier: 3.699A pdb=" N VAL G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS G 175 " --> pdb=" O ARG G 171 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 176 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 79 through 82 No H-bonds generated for 'chain 'F' and resid 79 through 82' Processing helix chain 'F' and resid 106 through 111 removed outlier: 3.644A pdb=" N ASP F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 177 removed outlier: 3.793A pdb=" N PHE F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 213 through 216 No H-bonds generated for 'chain 'F' and resid 213 through 216' Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 55 through 63 removed outlier: 3.670A pdb=" N LEU E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 83 No H-bonds generated for 'chain 'E' and resid 80 through 83' Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 163 through 170 removed outlier: 3.973A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 210 through 216 removed outlier: 3.750A pdb=" N GLU E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU E 215 " --> pdb=" O THR E 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.646A pdb=" N ARG B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 198 through 201 No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.702A pdb=" N MET B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 231' Processing helix chain 'H' and resid 43 through 51 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 129 through 143 removed outlier: 3.719A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR H 143 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 180 through 183 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 237 through 258 removed outlier: 3.800A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU H 244 " --> pdb=" O GLY H 240 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY H 247 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS H 248 " --> pdb=" O GLU H 244 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'H' and resid 299 through 302 removed outlier: 3.683A pdb=" N ARG H 302 " --> pdb=" O LEU H 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 299 through 302' Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing sheet with id= A, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= B, first strand: chain 'A' and resid 452 through 456 removed outlier: 3.980A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N THR A 483 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 652 through 654 removed outlier: 7.496A pdb=" N ALA A 611 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 612 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER A 584 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 569 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 152 through 155 removed outlier: 6.023A pdb=" N LYS G 7 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR G 202 " --> pdb=" O LYS G 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 146 through 149 Processing sheet with id= F, first strand: chain 'G' and resid 118 through 122 Processing sheet with id= G, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= H, first strand: chain 'F' and resid 146 through 149 Processing sheet with id= I, first strand: chain 'F' and resid 118 through 123 Processing sheet with id= J, first strand: chain 'E' and resid 199 through 202 removed outlier: 3.740A pdb=" N LEU E 151 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 11 through 14 Processing sheet with id= L, first strand: chain 'E' and resid 120 through 123 removed outlier: 3.585A pdb=" N GLU E 123 " --> pdb=" O ARG E 136 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 6 through 9 Processing sheet with id= N, first strand: chain 'B' and resid 71 through 73 Processing sheet with id= O, first strand: chain 'B' and resid 128 through 131 Processing sheet with id= P, first strand: chain 'B' and resid 265 through 267 Processing sheet with id= Q, first strand: chain 'H' and resid 10 through 13 Processing sheet with id= R, first strand: chain 'H' and resid 37 through 41 Processing sheet with id= S, first strand: chain 'H' and resid 184 through 186 Processing sheet with id= T, first strand: chain 'H' and resid 211 through 214 removed outlier: 4.204A pdb=" N LYS H 211 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 276 through 279 453 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 9.22 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: 3727 1.32 - 1.45: 5207 1.45 - 1.57: 10720 1.57 - 1.69: 140 1.69 - 1.81: 66 Bond restraints: 19860 Sorted by residual: bond pdb=" C4 ATP A 802 " pdb=" C5 ATP A 802 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.50e+01 bond pdb=" C4 ATP A 803 " pdb=" C5 ATP A 803 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP A 802 " pdb=" C6 ATP A 802 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C5 ATP A 803 " pdb=" C6 ATP A 803 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C8 ATP A 803 " pdb=" N7 ATP A 803 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.18e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 96.20 - 104.40: 454 104.40 - 112.60: 9955 112.60 - 120.81: 10576 120.81 - 129.01: 6026 129.01 - 137.21: 122 Bond angle restraints: 27133 Sorted by residual: angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 123.73 16.14 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 121.65 15.18 1.00e+00 1.00e+00 2.31e+02 angle pdb=" PB ATP A 803 " pdb=" O3B ATP A 803 " pdb=" PG ATP A 803 " ideal model delta sigma weight residual 139.87 126.01 13.86 1.00e+00 1.00e+00 1.92e+02 angle pdb=" PA ATP A 803 " pdb=" O3A ATP A 803 " pdb=" PB ATP A 803 " ideal model delta sigma weight residual 136.83 123.96 12.87 1.00e+00 1.00e+00 1.66e+02 angle pdb=" N ARG H 219 " pdb=" CA ARG H 219 " pdb=" C ARG H 219 " ideal model delta sigma weight residual 111.39 126.13 -14.74 1.38e+00 5.25e-01 1.14e+02 ... (remaining 27128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 11529 32.35 - 64.69: 198 64.69 - 97.04: 19 97.04 - 129.39: 0 129.39 - 161.73: 3 Dihedral angle restraints: 11749 sinusoidal: 5141 harmonic: 6608 Sorted by residual: dihedral pdb=" O4' C N 8 " pdb=" C1' C N 8 " pdb=" N1 C N 8 " pdb=" C2 C N 8 " ideal model delta sinusoidal sigma weight residual -128.00 33.73 -161.73 1 1.70e+01 3.46e-03 6.48e+01 dihedral pdb=" O4' C N 14 " pdb=" C1' C N 14 " pdb=" N1 C N 14 " pdb=" C2 C N 14 " ideal model delta sinusoidal sigma weight residual -128.00 8.67 -136.67 1 1.70e+01 3.46e-03 5.74e+01 dihedral pdb=" CA ASN A 639 " pdb=" C ASN A 639 " pdb=" N GLU A 640 " pdb=" CA GLU A 640 " ideal model delta harmonic sigma weight residual 180.00 142.78 37.22 0 5.00e+00 4.00e-02 5.54e+01 ... (remaining 11746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2922 0.132 - 0.264: 123 0.264 - 0.396: 13 0.396 - 0.528: 3 0.528 - 0.659: 1 Chirality restraints: 3062 Sorted by residual: chirality pdb=" CA TYR H 218 " pdb=" N TYR H 218 " pdb=" C TYR H 218 " pdb=" CB TYR H 218 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA PRO H 160 " pdb=" N PRO H 160 " pdb=" C PRO H 160 " pdb=" CB PRO H 160 " both_signs ideal model delta sigma weight residual False 2.72 2.21 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA TYR B 78 " pdb=" N TYR B 78 " pdb=" C TYR B 78 " pdb=" CB TYR B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 3059 not shown) Planarity restraints: 3243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 154 " -0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C ASN H 154 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN H 154 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP H 155 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 163 " 0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ASN H 163 " -0.068 2.00e-02 2.50e+03 pdb=" O ASN H 163 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS H 164 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.031 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 732 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.010 2.00e-02 2.50e+03 ... (remaining 3240 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 6 1.86 - 2.62: 343 2.62 - 3.38: 25712 3.38 - 4.14: 49123 4.14 - 4.90: 88617 Nonbonded interactions: 163801 Sorted by model distance: nonbonded pdb=" NH1 ARG E 81 " pdb=" OE1 GLN E 162 " model vdw 1.102 2.520 nonbonded pdb=" CZ ARG E 81 " pdb=" OE1 GLN E 162 " model vdw 1.434 3.270 nonbonded pdb=" NH1 ARG E 81 " pdb=" CD GLN E 162 " model vdw 1.711 3.350 nonbonded pdb=" CD2 LEU A 749 " pdb=" CD1 ILE E 29 " model vdw 1.748 3.880 nonbonded pdb=" O SER B 264 " pdb=" CE1 PHE B 266 " model vdw 1.804 3.340 ... (remaining 163796 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' } 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 \ 158 and (name N or name CA or name C or name O or name CB )) or resid 159 or (r \ esid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 t \ hrough 217)) selection = (chain 'G' and (resid 2 through 66 or resid 76 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 72 5.49 5 Mg 2 5.21 5 S 37 5.16 5 C 12090 2.51 5 N 3296 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.320 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: 3.860 Check model and map are aligned: 0.290 Process input model: 59.290 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.009 0.099 19860 Z= 0.567 Angle : 1.183 20.818 27133 Z= 0.686 Chirality : 0.068 0.659 3062 Planarity : 0.006 0.070 3243 Dihedral : 12.621 161.733 7487 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.44 % Favored : 89.43 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.65 (0.12), residues: 2232 helix: -4.34 (0.08), residues: 787 sheet: -3.24 (0.23), residues: 372 loop : -3.40 (0.14), residues: 1073 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 616 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 637 average time/residue: 0.4055 time to fit residues: 363.2303 Evaluate side-chains 315 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 304 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3411 time to fit residues: 8.6984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 207 optimal weight: 0.2980 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 312 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS A 504 ASN A 598 ASN A 661 ASN A 735 ASN G 85 ASN G 134 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN F 33 ASN F 144 ASN F 213 ASN E 134 ASN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 144 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 208 HIS B 284 HIS B 288 ASN H 154 ASN H 338 ASN H 339 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19860 Z= 0.182 Angle : 0.687 13.049 27133 Z= 0.357 Chirality : 0.043 0.305 3062 Planarity : 0.005 0.068 3243 Dihedral : 11.225 164.660 3265 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.02 % Favored : 91.94 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.14), residues: 2232 helix: -2.92 (0.13), residues: 797 sheet: -2.97 (0.26), residues: 313 loop : -3.11 (0.15), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 399 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 28 residues processed: 438 average time/residue: 0.3561 time to fit residues: 229.4291 Evaluate side-chains 326 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 298 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2203 time to fit residues: 13.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 207 optimal weight: 0.0980 chunk 224 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 205 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 661 ASN A 675 ASN G 159 ASN E 197 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN H 80 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 19860 Z= 0.151 Angle : 0.619 12.927 27133 Z= 0.318 Chirality : 0.041 0.274 3062 Planarity : 0.004 0.038 3243 Dihedral : 10.834 166.509 3265 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.38 % Favored : 91.58 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.15), residues: 2232 helix: -1.80 (0.16), residues: 805 sheet: -2.53 (0.27), residues: 316 loop : -2.87 (0.16), residues: 1111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 361 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 22 residues processed: 401 average time/residue: 0.3658 time to fit residues: 215.2751 Evaluate side-chains 309 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 287 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2068 time to fit residues: 10.9528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 0.0470 chunk 22 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN F 197 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN H 82 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19860 Z= 0.192 Angle : 0.615 12.692 27133 Z= 0.316 Chirality : 0.042 0.276 3062 Planarity : 0.003 0.035 3243 Dihedral : 10.690 166.962 3265 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.83 % Favored : 91.13 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.16), residues: 2232 helix: -1.08 (0.17), residues: 795 sheet: -2.38 (0.28), residues: 316 loop : -2.71 (0.16), residues: 1121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 319 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 343 average time/residue: 0.3826 time to fit residues: 195.5712 Evaluate side-chains 299 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 283 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2552 time to fit residues: 9.8276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN D 42 ASN F 144 ASN E 33 ASN E 213 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.060 19860 Z= 0.446 Angle : 0.757 15.463 27133 Z= 0.393 Chirality : 0.047 0.288 3062 Planarity : 0.005 0.057 3243 Dihedral : 11.237 165.523 3265 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.11 % Favored : 88.84 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.09 (0.16), residues: 2232 helix: -1.04 (0.17), residues: 800 sheet: -2.31 (0.27), residues: 341 loop : -2.76 (0.17), residues: 1091 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 301 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 31 residues processed: 339 average time/residue: 0.3475 time to fit residues: 176.5567 Evaluate side-chains 294 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 263 time to evaluate : 2.332 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2188 time to fit residues: 14.7637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.8980 chunk 198 optimal weight: 0.0170 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 504 ASN A 604 ASN A 639 ASN D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN B 161 ASN B 288 ASN H 80 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.183 Angle : 0.634 14.729 27133 Z= 0.323 Chirality : 0.042 0.284 3062 Planarity : 0.003 0.036 3243 Dihedral : 10.980 169.457 3265 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.60 % Favored : 91.35 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.17), residues: 2232 helix: -0.67 (0.18), residues: 809 sheet: -2.25 (0.27), residues: 329 loop : -2.58 (0.17), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 303 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 321 average time/residue: 0.3507 time to fit residues: 169.5429 Evaluate side-chains 275 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1928 time to fit residues: 6.7974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 368 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19860 Z= 0.229 Angle : 0.646 14.265 27133 Z= 0.330 Chirality : 0.042 0.279 3062 Planarity : 0.004 0.041 3243 Dihedral : 10.906 169.834 3265 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.04 % Favored : 89.92 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.17), residues: 2232 helix: -0.50 (0.18), residues: 808 sheet: -2.21 (0.27), residues: 349 loop : -2.57 (0.18), residues: 1075 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 277 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 291 average time/residue: 0.3727 time to fit residues: 163.9134 Evaluate side-chains 275 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2595 time to fit residues: 7.4577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 172 optimal weight: 0.0670 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 263 ASN A 368 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.223 Angle : 0.643 14.060 27133 Z= 0.327 Chirality : 0.042 0.282 3062 Planarity : 0.003 0.034 3243 Dihedral : 10.874 170.383 3265 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.18 % Favored : 90.77 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.17), residues: 2232 helix: -0.37 (0.19), residues: 807 sheet: -2.15 (0.27), residues: 341 loop : -2.56 (0.18), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 279 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 291 average time/residue: 0.3548 time to fit residues: 154.5738 Evaluate side-chains 265 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 258 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1764 time to fit residues: 5.4000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 661 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.202 Angle : 0.639 13.920 27133 Z= 0.324 Chirality : 0.042 0.280 3062 Planarity : 0.003 0.035 3243 Dihedral : 10.819 170.501 3265 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.55 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.17), residues: 2232 helix: -0.16 (0.19), residues: 801 sheet: -2.22 (0.26), residues: 361 loop : -2.54 (0.18), residues: 1070 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 294 average time/residue: 0.3544 time to fit residues: 155.8053 Evaluate side-chains 269 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 265 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2016 time to fit residues: 4.4692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 0.0270 chunk 143 optimal weight: 4.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN E 159 ASN E 213 ASN B 288 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19860 Z= 0.187 Angle : 0.641 13.575 27133 Z= 0.324 Chirality : 0.041 0.276 3062 Planarity : 0.003 0.034 3243 Dihedral : 10.773 171.173 3265 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.96 % Favored : 90.99 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.17), residues: 2232 helix: -0.06 (0.19), residues: 800 sheet: -2.21 (0.26), residues: 355 loop : -2.56 (0.18), residues: 1077 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 274 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 279 average time/residue: 0.3632 time to fit residues: 151.6657 Evaluate side-chains 268 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 263 time to evaluate : 2.188 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1961 time to fit residues: 5.0127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.0170 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 312 ASN A 368 GLN D 42 ASN B 273 GLN B 288 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109756 restraints weight = 35819.060| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.13 r_work: 0.3317 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.169 Angle : 0.627 13.333 27133 Z= 0.316 Chirality : 0.041 0.276 3062 Planarity : 0.003 0.036 3243 Dihedral : 10.704 171.727 3265 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.01 % Favored : 90.95 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2232 helix: 0.03 (0.19), residues: 802 sheet: -2.14 (0.26), residues: 344 loop : -2.51 (0.17), residues: 1086 =============================================================================== Job complete usr+sys time: 4315.27 seconds wall clock time: 79 minutes 3.20 seconds (4743.20 seconds total)