Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 09:35:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/07_2023/6ifl_9654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/07_2023/6ifl_9654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/07_2023/6ifl_9654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/07_2023/6ifl_9654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/07_2023/6ifl_9654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/07_2023/6ifl_9654.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 38 5.16 5 C 11803 2.51 5 N 3187 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "E PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 6": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 18845 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5437 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 681} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 114 Chain: "B" 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: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1698 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 209} 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: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1607 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 198} Chain breaks: 1 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: "G" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2171 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "H" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2792 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 18} Chain: "J" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 752 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 4, 'rna3p': 30} Time building chain proxies: 9.42, per 1000 atoms: 0.50 Number of scatterers: 18845 At special positions: 0 Unit cell: (93.6, 132.08, 176.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 70 15.00 O 3747 8.00 N 3187 7.00 C 11803 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: 7.46 Conformation dependent library (CDL) restraints added in 2.8 seconds 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4136 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 22 sheets defined 40.8% alpha, 13.0% beta 28 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 5.72 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.846A pdb=" N ASP A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.603A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 68 through 82 removed outlier: 4.237A pdb=" N ILE A 72 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 167 through 170 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.630A pdb=" N ASN A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 removed outlier: 3.676A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.719A pdb=" N PHE A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.565A pdb=" N ILE A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 291 removed outlier: 4.101A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 335 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.765A pdb=" N MET A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 355' Processing helix chain 'A' and resid 361 through 380 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 523 through 530 removed outlier: 4.206A pdb=" N MET A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 533 No H-bonds generated for 'chain 'A' and resid 531 through 533' Processing helix chain 'A' and resid 541 through 557 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 585 through 604 Processing helix chain 'A' and resid 623 through 640 removed outlier: 3.604A pdb=" N ASN A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.594A pdb=" N GLN A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.617A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) 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: 3.829A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.518A pdb=" N ALA B 13 " --> pdb=" O TYR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 53 removed outlier: 3.705A pdb=" N THR B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 79 removed outlier: 3.738A pdb=" N ARG B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.705A pdb=" N LYS B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.839A pdb=" N LYS B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'C' and resid 36 through 48 removed outlier: 3.717A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.733A pdb=" N GLU C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 77 removed outlier: 4.169A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.684A pdb=" N LEU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 removed outlier: 3.585A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 71 through 75 removed outlier: 4.076A pdb=" N ASP D 75 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.588A pdb=" N ASP D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 179 removed outlier: 3.831A pdb=" N VAL D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.969A pdb=" N GLY D 189 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 64 removed outlier: 3.739A pdb=" N LYS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.522A pdb=" N ARG E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 161 through 180 removed outlier: 3.795A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 179 " --> pdb=" O LYS E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.609A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'F' and resid 49 through 64 removed outlier: 4.095A pdb=" N LYS F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 84 Processing helix chain 'F' and resid 107 through 112 removed outlier: 3.667A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 179 removed outlier: 3.624A pdb=" N ILE F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 179 " --> pdb=" O LYS F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 removed outlier: 3.879A pdb=" N LEU F 215 " --> pdb=" O THR F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 45 through 55 removed outlier: 3.552A pdb=" N PHE G 49 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'G' and resid 197 through 202 removed outlier: 3.700A pdb=" N ASP G 202 " --> pdb=" O LEU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 232 removed outlier: 4.509A pdb=" N GLU G 226 " --> pdb=" O ASP G 222 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 53 Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.937A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 81 removed outlier: 3.744A pdb=" N PHE H 78 " --> pdb=" O ARG H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.737A pdb=" N GLY H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 removed outlier: 4.046A pdb=" N ILE H 167 " --> pdb=" O LYS H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'H' and resid 236 through 241 Processing helix chain 'H' and resid 245 through 260 removed outlier: 3.981A pdb=" N PHE H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 302 removed outlier: 3.597A pdb=" N ARG H 302 " --> pdb=" O ILE H 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 307 removed outlier: 3.681A pdb=" N ALA A 306 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 456 removed outlier: 6.051A pdb=" N SER A 467 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 570 through 574 removed outlier: 4.962A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 515 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 609 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N SER A 645 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA A 611 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.314A pdb=" N LYS D 5 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN D 11 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN D 197 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG D 13 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE D 195 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 118 through 122 Processing sheet with id=AA7, first strand: chain 'E' and resid 46 through 47 removed outlier: 3.923A pdb=" N PHE E 102 " --> pdb=" O ASP E 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 46 through 47 removed outlier: 3.923A pdb=" N PHE E 102 " --> pdb=" O ASP E 148 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE E 8 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS E 5 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR E 202 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS E 7 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 200 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER E 9 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU E 198 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 126 Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'F' and resid 46 through 47 removed outlier: 4.107A pdb=" N PHE F 102 " --> pdb=" O ASP F 148 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.772A pdb=" N VAL G 158 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'G' and resid 126 through 134 Processing sheet with id=AB7, first strand: chain 'G' and resid 204 through 205 Processing sheet with id=AB8, first strand: chain 'G' and resid 236 through 239 Processing sheet with id=AB9, first strand: chain 'G' and resid 273 through 274 removed outlier: 3.637A pdb=" N GLN G 273 " --> pdb=" O ALA G 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 184 through 186 removed outlier: 3.668A pdb=" N THR H 226 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AC4, first strand: chain 'H' and resid 212 through 214 removed outlier: 4.523A pdb=" N GLN H 201 " --> pdb=" O LYS H 320 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS H 320 " --> pdb=" O GLN H 201 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 6.28 Time building geometry restraints manager: 8.01 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: 3209 1.32 - 1.44: 5467 1.44 - 1.57: 10461 1.57 - 1.69: 138 1.69 - 1.82: 70 Bond restraints: 19345 Sorted by residual: bond pdb=" C SER A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.337 1.372 -0.035 1.24e-02 6.50e+03 8.12e+00 bond pdb=" CB ARG D 136 " pdb=" CG ARG D 136 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.02e+00 bond pdb=" C PHE H 159 " pdb=" N PRO H 160 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.76e+00 bond pdb=" CB GLU F 123 " pdb=" CG GLU F 123 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.18e+00 bond pdb=" CB VAL A 516 " pdb=" CG2 VAL A 516 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.43e+00 ... (remaining 19340 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.12: 534 105.12 - 112.39: 9263 112.39 - 119.65: 7121 119.65 - 126.92: 9190 126.92 - 134.19: 323 Bond angle restraints: 26431 Sorted by residual: angle pdb=" N ILE D 78 " pdb=" CA ILE D 78 " pdb=" C ILE D 78 " ideal model delta sigma weight residual 113.71 100.12 13.59 9.50e-01 1.11e+00 2.05e+02 angle pdb=" N THR F 130 " pdb=" CA THR F 130 " pdb=" C THR F 130 " ideal model delta sigma weight residual 111.00 131.20 -20.20 2.80e+00 1.28e-01 5.20e+01 angle pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 103.25 109.71 -6.46 1.05e+00 9.07e-01 3.79e+01 angle pdb=" C GLY H 21 " pdb=" N ASN H 22 " pdb=" CA ASN H 22 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" C ILE F 129 " pdb=" N THR F 130 " pdb=" CA THR F 130 " ideal model delta sigma weight residual 121.70 132.27 -10.57 1.80e+00 3.09e-01 3.45e+01 ... (remaining 26426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 11177 31.68 - 63.37: 264 63.37 - 95.05: 11 95.05 - 126.74: 2 126.74 - 158.42: 1 Dihedral angle restraints: 11455 sinusoidal: 5043 harmonic: 6412 Sorted by residual: dihedral pdb=" CA SER A 502 " pdb=" C SER A 502 " pdb=" N LYS A 503 " pdb=" CA LYS A 503 " ideal model delta harmonic sigma weight residual 180.00 113.54 66.46 0 5.00e+00 4.00e-02 1.77e+02 dihedral pdb=" CA ARG A 381 " pdb=" C ARG A 381 " pdb=" N TYR A 382 " pdb=" CA TYR A 382 " ideal model delta harmonic sigma weight residual 180.00 124.14 55.86 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLY A 488 " pdb=" C GLY A 488 " pdb=" N ASP A 489 " pdb=" CA ASP A 489 " ideal model delta harmonic sigma weight residual 180.00 -130.00 -50.00 0 5.00e+00 4.00e-02 1.00e+02 ... (remaining 11452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2399 0.077 - 0.153: 516 0.153 - 0.230: 68 0.230 - 0.306: 15 0.306 - 0.383: 7 Chirality restraints: 3005 Sorted by residual: chirality pdb=" CA THR F 130 " pdb=" N THR F 130 " pdb=" C THR F 130 " pdb=" CB THR F 130 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C1' G I 21 " pdb=" O4' G I 21 " pdb=" C2' G I 21 " pdb=" N9 G I 21 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 3002 not shown) Planarity restraints: 3137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.066 2.00e-02 2.50e+03 3.01e-02 2.49e+01 pdb=" N9 A I 27 " -0.071 2.00e-02 2.50e+03 pdb=" C8 A I 27 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.018 2.00e-02 2.50e+03 pdb=" N1 A I 27 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A I 27 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.062 2.00e-02 2.50e+03 2.70e-02 2.19e+01 pdb=" N9 G I 21 " -0.065 2.00e-02 2.50e+03 pdb=" C8 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.021 2.00e-02 2.50e+03 pdb=" N1 G I 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A I 7 " 0.060 2.00e-02 2.50e+03 2.61e-02 1.87e+01 pdb=" N9 A I 7 " -0.056 2.00e-02 2.50e+03 pdb=" C8 A I 7 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A I 7 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 7 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A I 7 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A I 7 " 0.017 2.00e-02 2.50e+03 pdb=" N1 A I 7 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A I 7 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A I 7 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A I 7 " -0.011 2.00e-02 2.50e+03 ... (remaining 3134 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2332 2.74 - 3.28: 17888 3.28 - 3.82: 32560 3.82 - 4.36: 40388 4.36 - 4.90: 67031 Nonbonded interactions: 160199 Sorted by model distance: nonbonded pdb=" O PHE G 71 " pdb=" OH TYR G 157 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR A 256 " pdb=" OH TYR A 573 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR D 153 " pdb=" OD2 ASP D 166 " model vdw 2.247 2.440 nonbonded pdb=" OD2 ASP G 62 " pdb=" OG SER G 262 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR G 61 " pdb=" O LEU G 215 " model vdw 2.263 2.440 ... (remaining 160194 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 65 or resid 77 through 157 or (resid 158 and (na \ me N or name CA or name C or name O or name CB )) or resid 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 'E' and (resid 2 through 65 or resid 77 through 217)) selection = chain 'F' } 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 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.550 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 52.210 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.010 0.090 19345 Z= 0.621 Angle : 1.269 20.197 26431 Z= 0.686 Chirality : 0.067 0.383 3005 Planarity : 0.007 0.072 3137 Dihedral : 13.060 158.424 7319 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.17 % Favored : 87.41 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.82 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.14), residues: 2161 helix: -3.03 (0.12), residues: 826 sheet: -2.61 (0.26), residues: 319 loop : -3.32 (0.15), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 561 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 570 average time/residue: 0.3796 time to fit residues: 306.3328 Evaluate side-chains 305 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1735 time to fit residues: 3.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 ASN A 129 ASN A 158 ASN A 268 GLN A 329 GLN A 391 ASN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN A 676 HIS A 735 ASN B 23 ASN B 26 ASN D 85 ASN D 161 ASN E 33 ASN E 105 ASN F 33 ASN G 104 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 161 ASN G 174 GLN G 273 GLN G 284 HIS ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN H 163 ASN H 210 ASN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19345 Z= 0.238 Angle : 0.762 14.260 26431 Z= 0.400 Chirality : 0.046 0.334 3005 Planarity : 0.005 0.076 3137 Dihedral : 11.945 154.932 3223 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.92 % Favored : 88.94 % Rotamer Outliers : 4.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -3.47 (0.16), residues: 2161 helix: -1.57 (0.16), residues: 825 sheet: -2.27 (0.27), residues: 308 loop : -2.93 (0.17), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 353 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 26 residues processed: 410 average time/residue: 0.3492 time to fit residues: 210.7919 Evaluate side-chains 313 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 287 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1906 time to fit residues: 11.6723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 167 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS A 51 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN D 33 ASN E 105 ASN G 104 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN ** 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: 0.7899 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19345 Z= 0.191 Angle : 0.701 14.057 26431 Z= 0.365 Chirality : 0.045 0.340 3005 Planarity : 0.004 0.053 3137 Dihedral : 11.590 153.667 3223 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.38 % Favored : 88.52 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.81 (0.17), residues: 2161 helix: -0.78 (0.17), residues: 826 sheet: -2.13 (0.27), residues: 323 loop : -2.71 (0.18), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 343 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 21 residues processed: 390 average time/residue: 0.3413 time to fit residues: 198.2575 Evaluate side-chains 293 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 272 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1922 time to fit residues: 10.1031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 192 optimal weight: 0.0970 chunk 57 optimal weight: 0.3980 overall best weight: 3.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN A 175 ASN A 189 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN E 105 ASN E 206 ASN F 162 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS H 22 ASN H 73 ASN H 115 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 19345 Z= 0.347 Angle : 0.756 14.068 26431 Z= 0.395 Chirality : 0.048 0.365 3005 Planarity : 0.005 0.058 3137 Dihedral : 11.538 153.440 3223 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.48 % Favored : 88.39 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.54 (0.17), residues: 2161 helix: -0.41 (0.18), residues: 816 sheet: -1.96 (0.26), residues: 352 loop : -2.71 (0.18), residues: 993 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 2.061 Fit side-chains outliers start: 55 outliers final: 30 residues processed: 337 average time/residue: 0.3459 time to fit residues: 174.5315 Evaluate side-chains 297 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1849 time to fit residues: 13.0970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN G 12 ASN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN ** 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: 0.7985 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19345 Z= 0.248 Angle : 0.708 13.529 26431 Z= 0.368 Chirality : 0.046 0.347 3005 Planarity : 0.004 0.055 3137 Dihedral : 11.479 152.504 3223 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.85 % Favored : 88.06 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.35 (0.17), residues: 2161 helix: -0.10 (0.18), residues: 814 sheet: -1.97 (0.26), residues: 347 loop : -2.70 (0.17), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 293 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 310 average time/residue: 0.3330 time to fit residues: 154.4425 Evaluate side-chains 290 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 275 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1968 time to fit residues: 8.0160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 19345 Z= 0.263 Angle : 0.705 13.474 26431 Z= 0.367 Chirality : 0.045 0.348 3005 Planarity : 0.004 0.051 3137 Dihedral : 11.393 152.552 3223 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.43 % Favored : 88.48 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.21 (0.17), residues: 2161 helix: 0.07 (0.18), residues: 817 sheet: -1.91 (0.26), residues: 355 loop : -2.65 (0.18), residues: 989 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 296 time to evaluate : 1.979 Fit side-chains outliers start: 34 outliers final: 13 residues processed: 319 average time/residue: 0.3297 time to fit residues: 157.4642 Evaluate side-chains 279 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 266 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1906 time to fit residues: 7.3531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN H 3 ASN ** 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: 0.7959 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19345 Z= 0.203 Angle : 0.691 12.678 26431 Z= 0.356 Chirality : 0.044 0.333 3005 Planarity : 0.004 0.047 3137 Dihedral : 11.321 151.645 3223 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.34 % Favored : 88.62 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.04 (0.17), residues: 2161 helix: 0.27 (0.18), residues: 815 sheet: -1.84 (0.27), residues: 340 loop : -2.61 (0.17), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 298 time to evaluate : 2.089 Fit side-chains outliers start: 26 outliers final: 9 residues processed: 314 average time/residue: 0.3444 time to fit residues: 160.3241 Evaluate side-chains 277 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 268 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1716 time to fit residues: 5.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN G 11 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** 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: 0.8066 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 19345 Z= 0.415 Angle : 0.796 14.274 26431 Z= 0.410 Chirality : 0.049 0.393 3005 Planarity : 0.005 0.055 3137 Dihedral : 11.406 153.510 3223 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.40 % Favored : 87.55 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.05 (0.17), residues: 2161 helix: 0.19 (0.18), residues: 809 sheet: -1.70 (0.26), residues: 342 loop : -2.59 (0.18), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 260 time to evaluate : 2.114 Fit side-chains outliers start: 34 outliers final: 17 residues processed: 286 average time/residue: 0.3567 time to fit residues: 152.5145 Evaluate side-chains 267 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 250 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2027 time to fit residues: 9.3974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN F 162 GLN G 11 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 19345 Z= 0.243 Angle : 0.719 13.118 26431 Z= 0.372 Chirality : 0.046 0.347 3005 Planarity : 0.004 0.053 3137 Dihedral : 11.376 152.217 3223 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.48 % Favored : 88.48 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.00 (0.17), residues: 2161 helix: 0.31 (0.18), residues: 810 sheet: -1.83 (0.26), residues: 355 loop : -2.58 (0.18), residues: 996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 274 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 280 average time/residue: 0.3451 time to fit residues: 144.6256 Evaluate side-chains 263 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 257 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1742 time to fit residues: 4.7187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 176 optimal weight: 0.0870 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN G 11 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19345 Z= 0.170 Angle : 0.676 11.536 26431 Z= 0.350 Chirality : 0.044 0.321 3005 Planarity : 0.004 0.039 3137 Dihedral : 11.190 151.454 3223 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.11 % Favored : 88.85 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.18), residues: 2161 helix: 0.49 (0.18), residues: 819 sheet: -1.80 (0.26), residues: 357 loop : -2.55 (0.18), residues: 985 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 297 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 298 average time/residue: 0.3494 time to fit residues: 155.2354 Evaluate side-chains 272 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2005 time to fit residues: 3.5507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 162 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 GLN ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116695 restraints weight = 27611.875| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.31 r_work: 0.3178 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19345 Z= 0.166 Angle : 0.670 11.037 26431 Z= 0.346 Chirality : 0.043 0.313 3005 Planarity : 0.003 0.037 3137 Dihedral : 11.090 150.361 3223 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.92 % Favored : 89.03 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.73 (0.18), residues: 2161 helix: 0.60 (0.18), residues: 817 sheet: -1.74 (0.26), residues: 353 loop : -2.49 (0.18), residues: 991 =============================================================================== Job complete usr+sys time: 4125.49 seconds wall clock time: 75 minutes 49.21 seconds (4549.21 seconds total)