Starting phenix.real_space_refine on Sun Mar 17 20:20:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/03_2024/6ifl_9654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/03_2024/6ifl_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_9654/03_2024/6ifl_9654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/03_2024/6ifl_9654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/03_2024/6ifl_9654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifl_9654/03_2024/6ifl_9654.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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-dev-5265/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: 10.65, per 1000 atoms: 0.57 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: 7.59 Conformation dependent library (CDL) restraints added in 3.4 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: 6.24 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: 6.08 Time building geometry restraints manager: 8.18 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: 11282 31.68 - 63.37: 351 63.37 - 95.05: 45 95.05 - 126.74: 2 126.74 - 158.42: 1 Dihedral angle restraints: 11681 sinusoidal: 5269 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 11678 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: 0.430 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: 2.890 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 54.690 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.140 ------------------------------------------------------------------------------- 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 : 14.828 158.424 7545 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 % Allowed : 7.84 % Favored : 91.06 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.006 TRP A 732 HIS 0.017 0.003 HIS A 695 PHE 0.043 0.004 PHE A 655 TYR 0.047 0.003 TYR A 663 ARG 0.034 0.002 ARG A 121 *********************** 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 : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ILE cc_start: 0.8931 (mm) cc_final: 0.8613 (mt) REVERT: A 242 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8195 (pt) REVERT: A 663 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6471 (m-10) REVERT: B 22 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.7143 (mtp85) REVERT: B 49 THR cc_start: 0.7742 (t) cc_final: 0.7510 (p) REVERT: B 57 LYS cc_start: 0.8363 (mttt) cc_final: 0.8160 (mttt) REVERT: C 52 ASP cc_start: 0.8210 (m-30) cc_final: 0.8007 (m-30) REVERT: C 60 ASP cc_start: 0.7921 (m-30) cc_final: 0.7643 (m-30) REVERT: C 81 ILE cc_start: 0.7144 (tt) cc_final: 0.6735 (tt) REVERT: C 84 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8219 (ttpt) REVERT: D 100 ASP cc_start: 0.7479 (m-30) cc_final: 0.7168 (m-30) REVERT: D 126 ILE cc_start: 0.8027 (mt) cc_final: 0.7817 (mt) REVERT: E 7 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8057 (ttpp) REVERT: E 67 LYS cc_start: 0.8426 (pttm) cc_final: 0.7901 (ptmm) REVERT: F 117 TYR cc_start: 0.8408 (m-80) cc_final: 0.8012 (m-80) REVERT: F 211 THR cc_start: 0.8831 (t) cc_final: 0.8602 (m) REVERT: G 113 ASP cc_start: 0.7280 (m-30) cc_final: 0.6903 (m-30) REVERT: H 114 VAL cc_start: 0.9247 (m) cc_final: 0.8966 (t) outliers start: 20 outliers final: 1 residues processed: 570 average time/residue: 0.3739 time to fit residues: 301.4269 Evaluate side-chains 311 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 308 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain H residue 132 LEU 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: 0.7980 chunk 174 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7900 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19345 Z= 0.215 Angle : 0.745 14.056 26431 Z= 0.392 Chirality : 0.046 0.333 3005 Planarity : 0.005 0.077 3137 Dihedral : 15.963 154.784 3455 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.97 % Favored : 88.94 % Rotamer: Outliers : 4.30 % Allowed : 12.53 % Favored : 83.17 % 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: -3.48 (0.16), residues: 2161 helix: -1.54 (0.16), residues: 827 sheet: -2.36 (0.26), residues: 322 loop : -2.94 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 732 HIS 0.010 0.001 HIS A 55 PHE 0.020 0.002 PHE A 348 TYR 0.027 0.002 TYR A 300 ARG 0.005 0.001 ARG D 188 *********************** 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 441 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 363 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8571 (mt) REVERT: A 663 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: C 52 ASP cc_start: 0.8239 (m-30) cc_final: 0.7923 (m-30) REVERT: C 60 ASP cc_start: 0.8044 (m-30) cc_final: 0.7791 (m-30) REVERT: C 81 ILE cc_start: 0.6679 (tt) cc_final: 0.6212 (tt) REVERT: D 18 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8679 (pt) REVERT: D 100 ASP cc_start: 0.7473 (m-30) cc_final: 0.7048 (m-30) REVERT: D 126 ILE cc_start: 0.7439 (mt) cc_final: 0.7116 (mt) REVERT: D 176 LEU cc_start: 0.8724 (mm) cc_final: 0.8363 (mp) REVERT: E 7 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8143 (ttpp) REVERT: E 67 LYS cc_start: 0.8663 (pttm) cc_final: 0.8057 (ptmm) REVERT: E 163 VAL cc_start: 0.8529 (p) cc_final: 0.8276 (t) REVERT: F 117 TYR cc_start: 0.8385 (m-80) cc_final: 0.7893 (m-80) REVERT: F 210 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7911 (mtpt) REVERT: G 3 TYR cc_start: 0.7752 (m-80) cc_final: 0.7547 (m-80) REVERT: G 113 ASP cc_start: 0.7356 (m-30) cc_final: 0.7060 (m-30) REVERT: G 175 TYR cc_start: 0.8476 (m-80) cc_final: 0.8232 (m-80) REVERT: G 219 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8968 (tp) REVERT: G 234 TYR cc_start: 0.8183 (p90) cc_final: 0.7814 (p90) REVERT: H 114 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8985 (t) REVERT: H 141 MET cc_start: 0.8239 (mtp) cc_final: 0.8028 (mtp) outliers start: 78 outliers final: 29 residues processed: 422 average time/residue: 0.3296 time to fit residues: 205.3831 Evaluate side-chains 331 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 297 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 43 ASN Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 315 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 162 optimal weight: 0.0370 overall best weight: 1.7662 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 161 ASN E 105 ASN G 104 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN H 65 GLN H 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 0.061 19345 Z= 0.224 Angle : 0.709 14.284 26431 Z= 0.370 Chirality : 0.045 0.337 3005 Planarity : 0.004 0.055 3137 Dihedral : 15.684 153.451 3455 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.29 % Favored : 88.57 % Rotamer: Outliers : 4.25 % Allowed : 13.74 % Favored : 82.01 % 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: -2.79 (0.17), residues: 2161 helix: -0.76 (0.17), residues: 818 sheet: -2.06 (0.26), residues: 347 loop : -2.72 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 732 HIS 0.007 0.001 HIS A 55 PHE 0.022 0.001 PHE A 235 TYR 0.022 0.001 TYR A 300 ARG 0.004 0.001 ARG F 81 *********************** 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 411 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 334 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6534 (t-100) cc_final: 0.6061 (t-100) REVERT: A 663 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: B 22 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7381 (mtp180) REVERT: B 94 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 52 ASP cc_start: 0.8235 (m-30) cc_final: 0.7915 (m-30) REVERT: C 60 ASP cc_start: 0.8070 (m-30) cc_final: 0.7810 (m-30) REVERT: C 63 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8264 (mt) REVERT: D 18 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8694 (pt) REVERT: D 100 ASP cc_start: 0.7374 (m-30) cc_final: 0.6980 (m-30) REVERT: D 126 ILE cc_start: 0.7232 (mt) cc_final: 0.6834 (mt) REVERT: E 1 MET cc_start: 0.5201 (tpp) cc_final: 0.4488 (tpp) REVERT: E 7 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8163 (ttpp) REVERT: E 67 LYS cc_start: 0.8708 (pttm) cc_final: 0.8090 (ptmm) REVERT: E 107 ASP cc_start: 0.7625 (p0) cc_final: 0.7379 (p0) REVERT: F 11 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7898 (mm-40) REVERT: F 117 TYR cc_start: 0.8362 (m-80) cc_final: 0.7907 (m-10) REVERT: F 143 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7681 (ttp80) REVERT: F 210 LYS cc_start: 0.8372 (mtmm) cc_final: 0.7900 (mtpt) REVERT: G 3 TYR cc_start: 0.7712 (m-80) cc_final: 0.7500 (m-80) REVERT: G 113 ASP cc_start: 0.7397 (m-30) cc_final: 0.7087 (m-30) REVERT: G 219 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9036 (tp) REVERT: G 234 TYR cc_start: 0.8185 (p90) cc_final: 0.7803 (p90) REVERT: G 258 TYR cc_start: 0.8714 (m-80) cc_final: 0.8479 (m-80) REVERT: H 65 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6944 (pp30) REVERT: H 114 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.9007 (t) outliers start: 77 outliers final: 40 residues processed: 392 average time/residue: 0.3186 time to fit residues: 187.3306 Evaluate side-chains 333 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 286 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 3.9990 chunk 151 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 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 22 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19345 Z= 0.259 Angle : 0.706 13.888 26431 Z= 0.370 Chirality : 0.046 0.346 3005 Planarity : 0.004 0.054 3137 Dihedral : 15.587 152.458 3455 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.20 % Rotamer: Outliers : 5.02 % Allowed : 14.96 % Favored : 80.02 % 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: -2.54 (0.17), residues: 2161 helix: -0.38 (0.18), residues: 819 sheet: -1.96 (0.27), residues: 339 loop : -2.74 (0.17), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.018 0.001 PHE A 246 TYR 0.024 0.002 TYR A 363 ARG 0.005 0.001 ARG A 550 *********************** 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 401 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 310 time to evaluate : 2.189 Fit side-chains REVERT: A 38 TRP cc_start: 0.6553 (t-100) cc_final: 0.6074 (t-100) REVERT: A 663 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: B 22 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7286 (mtp180) REVERT: C 52 ASP cc_start: 0.8225 (m-30) cc_final: 0.7923 (m-30) REVERT: C 60 ASP cc_start: 0.8082 (m-30) cc_final: 0.7783 (m-30) REVERT: C 63 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8340 (mt) REVERT: C 84 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8089 (ttpt) REVERT: D 18 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8740 (pt) REVERT: D 100 ASP cc_start: 0.7474 (m-30) cc_final: 0.7081 (m-30) REVERT: D 117 TYR cc_start: 0.8919 (m-80) cc_final: 0.8650 (m-80) REVERT: D 126 ILE cc_start: 0.7237 (mt) cc_final: 0.6859 (mt) REVERT: E 1 MET cc_start: 0.5234 (tpp) cc_final: 0.4827 (mtm) REVERT: E 7 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8176 (ttpp) REVERT: E 67 LYS cc_start: 0.8760 (pttm) cc_final: 0.8116 (ptmm) REVERT: E 107 ASP cc_start: 0.7644 (p0) cc_final: 0.7349 (p0) REVERT: F 11 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8192 (mm110) REVERT: F 117 TYR cc_start: 0.8412 (m-80) cc_final: 0.7982 (m-10) REVERT: F 143 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7799 (ttp80) REVERT: F 168 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7671 (tppt) REVERT: F 210 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7914 (mtpt) REVERT: G 3 TYR cc_start: 0.7753 (m-80) cc_final: 0.7455 (m-80) REVERT: G 113 ASP cc_start: 0.7403 (m-30) cc_final: 0.7097 (m-30) REVERT: G 219 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9084 (tp) REVERT: G 234 TYR cc_start: 0.8267 (p90) cc_final: 0.7889 (p90) REVERT: H 114 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8943 (t) outliers start: 91 outliers final: 61 residues processed: 375 average time/residue: 0.3279 time to fit residues: 182.8546 Evaluate side-chains 355 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 288 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 43 ASN Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 310 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 189 ASN ** 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** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19345 Z= 0.220 Angle : 0.679 13.191 26431 Z= 0.355 Chirality : 0.044 0.339 3005 Planarity : 0.004 0.049 3137 Dihedral : 15.483 151.365 3453 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.20 % Rotamer: Outliers : 4.64 % Allowed : 15.56 % Favored : 79.80 % 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: -2.34 (0.17), residues: 2161 helix: -0.06 (0.18), residues: 819 sheet: -2.01 (0.26), residues: 339 loop : -2.70 (0.17), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.016 0.001 PHE E 167 TYR 0.020 0.001 TYR A 300 ARG 0.005 0.000 ARG A 550 *********************** 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 386 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 302 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6573 (t-100) cc_final: 0.6099 (t-100) REVERT: A 71 TYR cc_start: 0.7540 (m-80) cc_final: 0.7311 (m-80) REVERT: A 663 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: B 22 ARG cc_start: 0.7520 (mtp180) cc_final: 0.7222 (mtp180) REVERT: B 57 LYS cc_start: 0.8311 (mttt) cc_final: 0.7898 (mtpt) REVERT: C 52 ASP cc_start: 0.8236 (m-30) cc_final: 0.7920 (m-30) REVERT: C 60 ASP cc_start: 0.8036 (m-30) cc_final: 0.7759 (m-30) REVERT: C 63 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8315 (mt) REVERT: C 84 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8222 (ttpt) REVERT: D 18 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8733 (pt) REVERT: D 100 ASP cc_start: 0.7415 (m-30) cc_final: 0.6989 (m-30) REVERT: D 117 TYR cc_start: 0.8952 (m-80) cc_final: 0.8694 (m-80) REVERT: D 126 ILE cc_start: 0.7061 (mt) cc_final: 0.6651 (mt) REVERT: E 1 MET cc_start: 0.5312 (tpp) cc_final: 0.4882 (mtm) REVERT: E 7 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8153 (ttpp) REVERT: E 67 LYS cc_start: 0.8775 (pttm) cc_final: 0.8120 (ptmm) REVERT: E 193 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7951 (m) REVERT: E 212 LEU cc_start: 0.7913 (tp) cc_final: 0.7712 (tp) REVERT: F 11 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8118 (mm110) REVERT: F 117 TYR cc_start: 0.8379 (m-80) cc_final: 0.7901 (m-10) REVERT: F 143 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7864 (ttp80) REVERT: F 168 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7587 (tppt) REVERT: F 210 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7932 (mtpt) REVERT: G 113 ASP cc_start: 0.7407 (m-30) cc_final: 0.7108 (m-30) REVERT: G 157 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8074 (p90) REVERT: G 219 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9112 (tp) REVERT: G 258 TYR cc_start: 0.8798 (m-80) cc_final: 0.8558 (m-80) REVERT: H 42 ASP cc_start: 0.7758 (t70) cc_final: 0.7546 (t70) REVERT: H 65 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6582 (pp30) REVERT: H 114 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8933 (t) REVERT: H 307 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7324 (pmmt) outliers start: 84 outliers final: 59 residues processed: 366 average time/residue: 0.3187 time to fit residues: 175.3019 Evaluate side-chains 345 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 276 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 310 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 0.0670 chunk 42 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- 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 ** 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 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19345 Z= 0.238 Angle : 0.679 13.054 26431 Z= 0.355 Chirality : 0.045 0.342 3005 Planarity : 0.004 0.047 3137 Dihedral : 15.422 151.077 3453 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.15 % Favored : 88.76 % Rotamer: Outliers : 4.58 % Allowed : 16.83 % Favored : 78.59 % 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: -2.17 (0.17), residues: 2161 helix: 0.16 (0.18), residues: 814 sheet: -2.08 (0.27), residues: 333 loop : -2.62 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 732 HIS 0.007 0.001 HIS A 55 PHE 0.016 0.001 PHE A 246 TYR 0.021 0.002 TYR A 300 ARG 0.007 0.001 ARG A 550 *********************** 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 378 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 295 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6602 (t-100) cc_final: 0.6122 (t-100) REVERT: A 141 TYR cc_start: 0.7301 (m-10) cc_final: 0.7077 (m-80) REVERT: A 431 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: B 22 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7200 (mtp180) REVERT: B 57 LYS cc_start: 0.8181 (mttt) cc_final: 0.7877 (mttm) REVERT: B 84 LYS cc_start: 0.8764 (tptp) cc_final: 0.8428 (ttpt) REVERT: C 52 ASP cc_start: 0.8207 (m-30) cc_final: 0.7886 (m-30) REVERT: C 60 ASP cc_start: 0.8049 (m-30) cc_final: 0.7772 (m-30) REVERT: C 63 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8328 (mt) REVERT: C 84 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8202 (ttpt) REVERT: D 18 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8762 (pt) REVERT: D 100 ASP cc_start: 0.7333 (m-30) cc_final: 0.6887 (m-30) REVERT: D 126 ILE cc_start: 0.7054 (mt) cc_final: 0.6684 (mt) REVERT: E 1 MET cc_start: 0.5209 (tpp) cc_final: 0.4906 (mtm) REVERT: E 7 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8150 (ttpp) REVERT: E 67 LYS cc_start: 0.8784 (pttm) cc_final: 0.8122 (ptmm) REVERT: E 193 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (m) REVERT: E 212 LEU cc_start: 0.7917 (tp) cc_final: 0.7714 (tp) REVERT: F 11 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8099 (mm110) REVERT: F 42 THR cc_start: 0.8681 (p) cc_final: 0.8453 (t) REVERT: F 117 TYR cc_start: 0.8379 (m-80) cc_final: 0.7958 (m-10) REVERT: F 143 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7890 (ttp80) REVERT: F 210 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7939 (mtpt) REVERT: G 113 ASP cc_start: 0.7406 (m-30) cc_final: 0.7105 (m-30) REVERT: G 157 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8129 (p90) REVERT: G 219 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9128 (tp) REVERT: G 258 TYR cc_start: 0.8766 (m-80) cc_final: 0.8526 (m-80) REVERT: H 50 MET cc_start: 0.6927 (ppp) cc_final: 0.6524 (ppp) REVERT: H 65 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6525 (pp30) REVERT: H 114 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8913 (t) REVERT: H 307 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7311 (pmmt) outliers start: 83 outliers final: 64 residues processed: 358 average time/residue: 0.3300 time to fit residues: 176.7691 Evaluate side-chains 359 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 285 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 51 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3965 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 : 0.683 12.929 26431 Z= 0.356 Chirality : 0.045 0.346 3005 Planarity : 0.004 0.047 3137 Dihedral : 15.377 150.820 3453 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.29 % Favored : 88.66 % Rotamer: Outliers : 5.24 % Allowed : 16.78 % Favored : 77.98 % 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: 0.32 (0.18), residues: 811 sheet: -1.95 (0.27), residues: 339 loop : -2.61 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.021 0.001 PHE E 167 TYR 0.022 0.002 TYR A 300 ARG 0.005 0.001 ARG D 188 *********************** 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 382 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 287 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6578 (t-100) cc_final: 0.6098 (t-100) REVERT: A 224 TYR cc_start: 0.5589 (t80) cc_final: 0.5360 (t80) REVERT: A 431 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: A 663 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: B 22 ARG cc_start: 0.7508 (mtp180) cc_final: 0.7185 (mtp180) REVERT: C 52 ASP cc_start: 0.8213 (m-30) cc_final: 0.7889 (m-30) REVERT: C 60 ASP cc_start: 0.7930 (m-30) cc_final: 0.7719 (m-30) REVERT: D 18 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8797 (pt) REVERT: D 64 TYR cc_start: 0.8394 (m-80) cc_final: 0.7942 (m-80) REVERT: D 100 ASP cc_start: 0.7375 (m-30) cc_final: 0.6988 (m-30) REVERT: D 126 ILE cc_start: 0.7046 (mt) cc_final: 0.6670 (mt) REVERT: E 1 MET cc_start: 0.5140 (tpp) cc_final: 0.4849 (mtm) REVERT: E 7 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8136 (ttpp) REVERT: E 67 LYS cc_start: 0.8740 (pttm) cc_final: 0.8103 (ptmm) REVERT: E 128 ARG cc_start: 0.8724 (mmt90) cc_final: 0.8480 (mmt-90) REVERT: E 193 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.8037 (m) REVERT: E 212 LEU cc_start: 0.7913 (tp) cc_final: 0.7713 (tp) REVERT: F 11 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8100 (mm110) REVERT: F 42 THR cc_start: 0.8770 (p) cc_final: 0.8489 (t) REVERT: F 99 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7290 (ttt-90) REVERT: F 117 TYR cc_start: 0.8382 (m-80) cc_final: 0.7959 (m-10) REVERT: F 143 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7885 (ttp80) REVERT: F 168 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7764 (tppt) REVERT: F 177 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8619 (tt) REVERT: F 210 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7998 (mtpt) REVERT: G 113 ASP cc_start: 0.7419 (m-30) cc_final: 0.7121 (m-30) REVERT: G 219 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9129 (tp) REVERT: H 50 MET cc_start: 0.6864 (ppp) cc_final: 0.6507 (ppp) REVERT: H 65 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6522 (pp30) REVERT: H 114 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8900 (t) REVERT: H 166 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8706 (tt) REVERT: H 307 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7328 (pmmt) outliers start: 95 outliers final: 67 residues processed: 362 average time/residue: 0.3247 time to fit residues: 176.1016 Evaluate side-chains 347 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 268 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 145 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 168 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 336 GLN ** 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 F 162 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19345 Z= 0.193 Angle : 0.663 12.052 26431 Z= 0.344 Chirality : 0.044 0.333 3005 Planarity : 0.003 0.043 3137 Dihedral : 15.297 149.927 3453 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.29 % Favored : 88.66 % Rotamer: Outliers : 4.53 % Allowed : 17.33 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.91 (0.18), residues: 2161 helix: 0.47 (0.18), residues: 812 sheet: -1.89 (0.27), residues: 340 loop : -2.56 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.017 0.001 PHE A 548 TYR 0.029 0.001 TYR A 363 ARG 0.008 0.000 ARG A 550 *********************** 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 380 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 298 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6563 (t-100) cc_final: 0.6097 (t-100) REVERT: A 114 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6427 (m-80) REVERT: A 224 TYR cc_start: 0.5585 (t80) cc_final: 0.5334 (t80) REVERT: A 336 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7933 (mm110) REVERT: A 463 GLN cc_start: 0.7407 (tm-30) cc_final: 0.7090 (pp30) REVERT: B 22 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7272 (mtp180) REVERT: B 57 LYS cc_start: 0.8261 (mttt) cc_final: 0.7972 (mttp) REVERT: C 52 ASP cc_start: 0.8194 (m-30) cc_final: 0.7865 (m-30) REVERT: D 18 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8742 (pt) REVERT: D 100 ASP cc_start: 0.7322 (m-30) cc_final: 0.6868 (m-30) REVERT: E 1 MET cc_start: 0.5170 (tpp) cc_final: 0.4803 (mtm) REVERT: E 7 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8132 (ttpp) REVERT: E 67 LYS cc_start: 0.8730 (pttm) cc_final: 0.8096 (ptmm) REVERT: E 128 ARG cc_start: 0.8669 (mmt90) cc_final: 0.8419 (mmt-90) REVERT: E 193 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7895 (m) REVERT: F 11 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8043 (mm110) REVERT: F 42 THR cc_start: 0.8755 (p) cc_final: 0.8449 (t) REVERT: F 99 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7247 (ttt-90) REVERT: F 117 TYR cc_start: 0.8346 (m-80) cc_final: 0.7875 (m-10) REVERT: F 143 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7900 (ttp80) REVERT: F 177 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8581 (tt) REVERT: F 210 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7983 (mtpt) REVERT: G 219 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9123 (tp) REVERT: G 258 TYR cc_start: 0.8742 (m-80) cc_final: 0.8509 (m-80) REVERT: H 50 MET cc_start: 0.6912 (ppp) cc_final: 0.6533 (ppp) REVERT: H 114 VAL cc_start: 0.9184 (m) cc_final: 0.8935 (t) REVERT: H 166 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8698 (tt) REVERT: H 306 MET cc_start: 0.6415 (tpp) cc_final: 0.6026 (mmp) REVERT: H 307 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7298 (pmmt) outliers start: 82 outliers final: 57 residues processed: 365 average time/residue: 0.3295 time to fit residues: 179.0280 Evaluate side-chains 340 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 273 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19345 Z= 0.199 Angle : 0.666 11.951 26431 Z= 0.345 Chirality : 0.044 0.333 3005 Planarity : 0.003 0.042 3137 Dihedral : 15.251 149.795 3453 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.34 % Favored : 88.62 % Rotamer: Outliers : 4.14 % Allowed : 18.10 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.84 (0.18), residues: 2161 helix: 0.52 (0.18), residues: 815 sheet: -1.83 (0.27), residues: 337 loop : -2.53 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.034 0.001 PHE A 235 TYR 0.024 0.002 TYR A 384 ARG 0.005 0.000 ARG A 550 *********************** 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 346 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 271 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6495 (t-100) cc_final: 0.6032 (t-100) REVERT: A 114 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: A 224 TYR cc_start: 0.5616 (t80) cc_final: 0.5333 (t80) REVERT: B 22 ARG cc_start: 0.7601 (mtp180) cc_final: 0.7269 (mtp180) REVERT: B 57 LYS cc_start: 0.8266 (mttt) cc_final: 0.7979 (mttp) REVERT: C 52 ASP cc_start: 0.8185 (m-30) cc_final: 0.7873 (m-30) REVERT: D 18 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8760 (pt) REVERT: D 100 ASP cc_start: 0.7283 (m-30) cc_final: 0.6824 (m-30) REVERT: E 1 MET cc_start: 0.5176 (tpp) cc_final: 0.4808 (mtm) REVERT: E 7 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8152 (ttpp) REVERT: E 67 LYS cc_start: 0.8752 (pttm) cc_final: 0.8124 (ptmm) REVERT: E 193 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7896 (m) REVERT: F 11 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8042 (mm110) REVERT: F 42 THR cc_start: 0.8750 (p) cc_final: 0.8430 (t) REVERT: F 99 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7243 (ttt-90) REVERT: F 117 TYR cc_start: 0.8340 (m-80) cc_final: 0.7878 (m-10) REVERT: F 143 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7889 (ttp80) REVERT: F 168 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7818 (tppt) REVERT: F 177 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8582 (tt) REVERT: F 210 LYS cc_start: 0.8416 (mtmm) cc_final: 0.7988 (mtpt) REVERT: G 219 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9128 (tp) REVERT: H 114 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8931 (t) REVERT: H 166 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8693 (tt) REVERT: H 306 MET cc_start: 0.6280 (tpp) cc_final: 0.5945 (mmp) outliers start: 75 outliers final: 60 residues processed: 331 average time/residue: 0.3185 time to fit residues: 157.8459 Evaluate side-chains 329 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 260 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 176 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19345 Z= 0.228 Angle : 0.681 12.148 26431 Z= 0.353 Chirality : 0.044 0.340 3005 Planarity : 0.004 0.043 3137 Dihedral : 15.236 149.950 3453 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.06 % Favored : 88.89 % Rotamer: Outliers : 4.42 % Allowed : 17.77 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.80 (0.18), residues: 2161 helix: 0.55 (0.18), residues: 812 sheet: -1.73 (0.28), residues: 324 loop : -2.53 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.030 0.001 PHE A 235 TYR 0.030 0.002 TYR A 363 ARG 0.008 0.000 ARG A 550 ********************** 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 345 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 265 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.6494 (t-100) cc_final: 0.6031 (t-100) REVERT: A 114 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: A 224 TYR cc_start: 0.5843 (t80) cc_final: 0.5534 (t80) REVERT: B 22 ARG cc_start: 0.7583 (mtp180) cc_final: 0.7249 (mtp180) REVERT: B 57 LYS cc_start: 0.8279 (mttt) cc_final: 0.7986 (mttp) REVERT: C 52 ASP cc_start: 0.8192 (m-30) cc_final: 0.7871 (m-30) REVERT: D 18 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8788 (pt) REVERT: D 100 ASP cc_start: 0.7449 (m-30) cc_final: 0.7080 (m-30) REVERT: E 1 MET cc_start: 0.5162 (tpp) cc_final: 0.4774 (mtm) REVERT: E 7 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8155 (ttpp) REVERT: E 67 LYS cc_start: 0.8745 (pttm) cc_final: 0.8109 (ptmm) REVERT: E 193 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7965 (m) REVERT: F 11 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8057 (mm110) REVERT: F 42 THR cc_start: 0.8767 (p) cc_final: 0.8447 (t) REVERT: F 99 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7217 (ttt-90) REVERT: F 117 TYR cc_start: 0.8345 (m-80) cc_final: 0.7882 (m-10) REVERT: F 143 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7892 (ttp80) REVERT: F 168 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7840 (tppt) REVERT: F 177 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8560 (tt) REVERT: F 210 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7993 (mtpt) REVERT: G 219 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9118 (tp) REVERT: H 49 LYS cc_start: 0.8267 (tppt) cc_final: 0.8024 (tptm) REVERT: H 114 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8899 (t) REVERT: H 166 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8746 (tt) REVERT: H 306 MET cc_start: 0.6318 (tpp) cc_final: 0.5940 (mmp) REVERT: H 307 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7311 (pmmt) outliers start: 80 outliers final: 64 residues processed: 326 average time/residue: 0.3157 time to fit residues: 154.9952 Evaluate side-chains 337 residues out of total 1893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 263 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111846 restraints weight = 27569.817| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.33 r_work: 0.3099 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19345 Z= 0.218 Angle : 0.836 59.200 26431 Z= 0.465 Chirality : 0.044 0.334 3005 Planarity : 0.004 0.043 3137 Dihedral : 15.238 149.844 3453 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.15 % Favored : 88.80 % Rotamer: Outliers : 4.25 % Allowed : 18.10 % Favored : 77.65 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.78 (0.18), residues: 2161 helix: 0.57 (0.18), residues: 812 sheet: -1.73 (0.28), residues: 324 loop : -2.52 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.027 0.001 PHE A 235 TYR 0.022 0.002 TYR A 275 ARG 0.007 0.000 ARG A 550 =============================================================================== Job complete usr+sys time: 4337.86 seconds wall clock time: 78 minutes 58.79 seconds (4738.79 seconds total)