Starting phenix.real_space_refine on Sat Sep 12 21:15:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_9654.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_9654.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_9654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_9654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_9654.map" model { file = "/net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_9654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ifl_9654/09_2026/6ifl_9654.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 38 5.16 5 C 11803 2.51 5 N 3187 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 9, 'ASP:plan': 10, 'ASN:plan1': 4, 'GLN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 1, 'GLU:plan': 2} 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: {'ASP:plan': 1, 'GLU:plan': 2} 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: {'RNAv2': 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: {'RNAv2': 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: 4.07, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.67 Conformation dependent library (CDL) restraints added in 726.6 milliseconds 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: 2.63 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: 3.51 Time building geometry restraints manager: 2.19 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: 0.00 - 4.04: 25910 4.04 - 8.08: 475 8.08 - 12.12: 41 12.12 - 16.16: 4 16.16 - 20.20: 1 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 - 15.15: 10114 15.15 - 30.29: 890 30.29 - 45.44: 299 45.44 - 60.59: 121 60.59 - 75.73: 31 Dihedral angle restraints: 11455 sinusoidal: 5043 harmonic: 6412 Sorted by residual: dihedral pdb=" C4' A I 26 " pdb=" C3' A I 26 " pdb=" C2' A I 26 " pdb=" C1' A I 26 " ideal model delta sinusoidal sigma weight residual 36.34 -39.39 75.73 1 3.10e+00 1.04e-01 7.53e+02 dihedral pdb=" C4' G J 35 " pdb=" C3' G J 35 " pdb=" C2' G J 35 " pdb=" C1' G J 35 " ideal model delta sinusoidal sigma weight residual 36.34 -38.33 74.68 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" C4' G J 23 " pdb=" C3' G J 23 " pdb=" C2' G J 23 " pdb=" C1' G J 23 " ideal model delta sinusoidal sigma weight residual 36.34 -37.88 74.22 1 3.10e+00 1.04e-01 7.27e+02 ... (remaining 11452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2371 0.081 - 0.162: 462 0.162 - 0.243: 118 0.243 - 0.324: 43 0.324 - 0.405: 11 Chirality restraints: 3005 Sorted by residual: chirality pdb=" P G J 21 " pdb=" OP1 G J 21 " pdb=" OP2 G J 21 " pdb=" O5' G J 21 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.41 2.00e-01 2.50e+01 4.10e+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 2.46 2.07 0.39 2.00e-01 2.50e+01 3.72e+00 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 ... (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 3.040 nonbonded pdb=" OH TYR A 256 " pdb=" OH TYR A 573 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR D 153 " pdb=" OD2 ASP D 166 " model vdw 2.247 3.040 nonbonded pdb=" OD2 ASP G 62 " pdb=" OG SER G 262 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR G 61 " pdb=" O LEU G 215 " model vdw 2.263 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.740 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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= 0.428 Angle : 1.313 20.197 26431 Z= 0.689 Chirality : 0.080 0.405 3005 Planarity : 0.007 0.072 3137 Dihedral : 14.667 75.733 7319 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.17 % Favored : 87.41 % Rotamer: Outliers : 1.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.034 0.002 ARG A 121 TYR 0.047 0.003 TYR A 663 PHE 0.043 0.004 PHE A 655 TRP 0.071 0.006 TRP A 732 HIS 0.017 0.003 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00973 / 0.43 (19345) covalent geometry : angle 1.31305 / 0.69 (26431) hydrogen bonds : bond 0.16033 / 10.77 ( 729) hydrogen bonds : angle 7.60101 / 5.25 ( 2019) *********************** 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 to be fit. rotamer outliers: 20 poor density : 561 time to evaluate : 0.427 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: 0.8615 (mt) REVERT: A 242 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8196 (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: 0.7511 (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: 0.7167 (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: 0.7902 (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: 0.1784 time to fit residues: 145.8732 Evaluate side-chains 310 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 112 ASN A 129 ASN A 158 ASN A 175 ASN A 268 GLN A 329 GLN A 391 ASN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN A 676 HIS A 735 ASN B 23 ASN B 26 ASN D 85 ASN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN E 33 ASN E 134 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 249 ASN G 273 GLN G 284 HIS ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN H 82 ASN H 163 ASN H 210 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118465 restraints weight = 27407.209| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.91 r_work: 0.3234 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19345 Z= 0.178 Angle : 1.048 19.084 26431 Z= 0.482 Chirality : 0.097 2.080 3005 Planarity : 0.005 0.097 3137 Dihedral : 11.874 137.791 3229 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.97 % Favored : 88.89 % Rotamer: Outliers : 3.92 % Allowed : 12.47 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.16), residues: 2161 helix: -1.59 (0.16), residues: 825 sheet: -2.42 (0.26), residues: 317 loop : -2.98 (0.16), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 709 TYR 0.027 0.002 TYR A 300 PHE 0.020 0.002 PHE A 348 TRP 0.031 0.003 TRP A 732 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (19345) covalent geometry : angle 1.04755 / 0.48 (26431) hydrogen bonds : bond 0.04895 / 3.38 ( 729) hydrogen bonds : angle 5.69654 / 3.95 ( 2019) *********************** 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 448 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 377 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6779 (p0) cc_final: 0.6494 (t0) REVERT: A 130 LEU cc_start: 0.6335 (mm) cc_final: 0.6056 (mt) REVERT: A 146 LYS cc_start: 0.6629 (mttm) cc_final: 0.6372 (tppt) REVERT: A 392 ARG cc_start: 0.7137 (ptt90) cc_final: 0.6744 (tpm170) REVERT: A 541 THR cc_start: 0.8288 (m) cc_final: 0.8078 (p) REVERT: A 663 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6692 (m-10) REVERT: B 49 THR cc_start: 0.8036 (t) cc_final: 0.7334 (p) REVERT: B 53 GLU cc_start: 0.7954 (mp0) cc_final: 0.7514 (mp0) REVERT: C 52 ASP cc_start: 0.8433 (m-30) cc_final: 0.8149 (m-30) REVERT: C 60 ASP cc_start: 0.8504 (m-30) cc_final: 0.8171 (m-30) REVERT: C 81 ILE cc_start: 0.7029 (tt) cc_final: 0.6488 (tt) REVERT: C 84 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8346 (ttpt) REVERT: C 100 LYS cc_start: 0.8414 (pmmt) cc_final: 0.8051 (mtmm) REVERT: D 18 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8740 (pt) REVERT: D 126 ILE cc_start: 0.7573 (mt) cc_final: 0.7129 (mt) REVERT: D 176 LEU cc_start: 0.8764 (mm) cc_final: 0.8413 (mp) REVERT: E 1 MET cc_start: 0.5266 (tpt) cc_final: 0.4898 (tpp) REVERT: E 7 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8453 (ttpp) REVERT: E 67 LYS cc_start: 0.8870 (pttm) cc_final: 0.8274 (ptmm) REVERT: E 163 VAL cc_start: 0.8626 (p) cc_final: 0.8306 (t) REVERT: F 117 TYR cc_start: 0.8791 (m-80) cc_final: 0.8389 (m-80) REVERT: F 167 PHE cc_start: 0.8322 (m-80) cc_final: 0.8075 (m-80) REVERT: F 210 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8040 (mtpt) REVERT: G 3 TYR cc_start: 0.8079 (m-80) cc_final: 0.7847 (m-80) REVERT: G 113 ASP cc_start: 0.7612 (m-30) cc_final: 0.7349 (m-30) REVERT: G 219 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8956 (tp) REVERT: G 234 TYR cc_start: 0.8208 (p90) cc_final: 0.7879 (p90) REVERT: H 114 VAL cc_start: 0.9323 (m) cc_final: 0.9110 (t) REVERT: H 307 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6885 (pmmt) outliers start: 71 outliers final: 31 residues processed: 426 average time/residue: 0.1657 time to fit residues: 104.3463 Evaluate side-chains 342 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 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 483 THR Chi-restraints excluded: chain A residue 588 ILE 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 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 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 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 27 THR Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 307 LYS 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 202 optimal weight: 0.3980 chunk 2 optimal weight: 50.0000 chunk 88 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 193 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS A 450 ASN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN D 33 ASN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 161 ASN E 197 ASN E 206 ASN G 104 GLN G 134 ASN G 144 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS H 22 ASN H 115 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114949 restraints weight = 27629.502| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.90 r_work: 0.3193 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19345 Z= 0.196 Angle : 0.938 19.201 26431 Z= 0.439 Chirality : 0.084 1.949 3005 Planarity : 0.005 0.058 3137 Dihedral : 11.944 142.778 3229 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.34 % Favored : 88.57 % Rotamer: Outliers : 4.42 % Allowed : 13.52 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.17), residues: 2161 helix: -0.84 (0.17), residues: 825 sheet: -2.21 (0.26), residues: 337 loop : -2.75 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 295 TYR 0.024 0.002 TYR A 300 PHE 0.026 0.002 PHE A 235 TRP 0.026 0.002 TRP A 732 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (19345) covalent geometry : angle 0.93804 / 0.44 (26431) hydrogen bonds : bond 0.04585 / 3.09 ( 729) hydrogen bonds : angle 5.24171 / 3.65 ( 2019) *********************** 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 420 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 340 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.8288 (p) cc_final: 0.8043 (m) REVERT: A 38 TRP cc_start: 0.7141 (t-100) cc_final: 0.6591 (t-100) REVERT: A 50 ASP cc_start: 0.6910 (p0) cc_final: 0.6488 (t0) REVERT: A 196 ILE cc_start: 0.8659 (mm) cc_final: 0.8417 (mp) REVERT: A 392 ARG cc_start: 0.7395 (ptt90) cc_final: 0.7188 (tpm170) REVERT: A 450 ASN cc_start: 0.7835 (m-40) cc_final: 0.7627 (p0) REVERT: A 541 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 663 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: B 22 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7272 (mtp180) REVERT: B 36 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 68 TYR cc_start: 0.8658 (t80) cc_final: 0.8424 (t80) REVERT: C 25 ARG cc_start: 0.6192 (mmm-85) cc_final: 0.5596 (mpt180) REVERT: C 52 ASP cc_start: 0.8542 (m-30) cc_final: 0.8236 (m-30) REVERT: C 60 ASP cc_start: 0.8557 (m-30) cc_final: 0.8268 (m-30) REVERT: C 63 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8351 (mt) REVERT: C 81 ILE cc_start: 0.6851 (tt) cc_final: 0.6297 (tt) REVERT: C 84 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8295 (ttpt) REVERT: D 18 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8872 (pt) REVERT: D 126 ILE cc_start: 0.8057 (mt) cc_final: 0.7627 (mt) REVERT: E 1 MET cc_start: 0.5188 (tpt) cc_final: 0.4621 (mtm) REVERT: E 7 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8486 (ttpp) REVERT: E 67 LYS cc_start: 0.8970 (pttm) cc_final: 0.8337 (ptmm) REVERT: E 107 ASP cc_start: 0.8121 (p0) cc_final: 0.7775 (p0) REVERT: F 11 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8337 (mm-40) REVERT: F 117 TYR cc_start: 0.8865 (m-80) cc_final: 0.8350 (m-10) REVERT: F 143 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7816 (ttp80) REVERT: F 210 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8067 (mtpt) REVERT: G 113 ASP cc_start: 0.7710 (m-30) cc_final: 0.7412 (m-30) REVERT: G 219 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9091 (tp) REVERT: G 234 TYR cc_start: 0.8354 (p90) cc_final: 0.8074 (p90) REVERT: G 258 TYR cc_start: 0.8977 (m-80) cc_final: 0.8703 (m-80) REVERT: H 42 ASP cc_start: 0.8392 (t70) cc_final: 0.8094 (t70) REVERT: H 65 GLN cc_start: 0.7544 (pp30) cc_final: 0.7010 (pp30) REVERT: H 114 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9071 (t) outliers start: 80 outliers final: 40 residues processed: 401 average time/residue: 0.1598 time to fit residues: 95.7760 Evaluate side-chains 336 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 320 LEU 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 541 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 717 THR 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 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 F residue 36 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain G residue 61 THR 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 52 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR 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 35 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 GLN ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN A 189 ASN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN D 85 ASN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 ASN G 104 GLN G 134 ASN G 144 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113316 restraints weight = 27496.335| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.11 r_work: 0.3158 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19345 Z= 0.194 Angle : 0.892 17.185 26431 Z= 0.420 Chirality : 0.071 1.012 3005 Planarity : 0.004 0.058 3137 Dihedral : 12.233 140.809 3229 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.85 % Favored : 88.11 % Rotamer: Outliers : 4.86 % Allowed : 14.29 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.17), residues: 2161 helix: -0.40 (0.18), residues: 815 sheet: -2.20 (0.27), residues: 322 loop : -2.65 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 305 TYR 0.029 0.002 TYR G 157 PHE 0.018 0.002 PHE A 246 TRP 0.021 0.002 TRP A 732 HIS 0.006 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (19345) covalent geometry : angle 0.89241 / 0.42 (26431) hydrogen bonds : bond 0.04263 / 2.87 ( 729) hydrogen bonds : angle 5.07197 / 3.52 ( 2019) *********************** 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 397 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 309 time to evaluate : 0.704 Fit side-chains REVERT: A 38 TRP cc_start: 0.7191 (t-100) cc_final: 0.6621 (t-100) REVERT: A 50 ASP cc_start: 0.6772 (p0) cc_final: 0.6382 (t0) REVERT: A 392 ARG cc_start: 0.7028 (ptt90) cc_final: 0.6671 (tpm170) REVERT: A 528 MET cc_start: 0.5985 (mtt) cc_final: 0.5653 (ppp) REVERT: A 663 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: B 22 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7415 (mtp180) REVERT: B 57 LYS cc_start: 0.8457 (mttt) cc_final: 0.8128 (mttm) REVERT: B 75 TYR cc_start: 0.8490 (t80) cc_final: 0.8200 (t80) REVERT: C 52 ASP cc_start: 0.8576 (m-30) cc_final: 0.8298 (m-30) REVERT: C 60 ASP cc_start: 0.8596 (m-30) cc_final: 0.8323 (m-30) REVERT: C 63 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8443 (mt) REVERT: C 81 ILE cc_start: 0.6962 (tt) cc_final: 0.6314 (tt) REVERT: C 84 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8279 (ttpt) REVERT: D 18 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8861 (pt) REVERT: E 1 MET cc_start: 0.5268 (tpt) cc_final: 0.4665 (mtm) REVERT: E 7 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8474 (ttpp) REVERT: E 67 LYS cc_start: 0.8997 (pttm) cc_final: 0.8345 (ptmm) REVERT: E 107 ASP cc_start: 0.8070 (p0) cc_final: 0.7774 (p0) REVERT: E 163 VAL cc_start: 0.8676 (p) cc_final: 0.8327 (t) REVERT: F 11 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8588 (mm110) REVERT: F 117 TYR cc_start: 0.8924 (m-80) cc_final: 0.8449 (m-10) REVERT: F 210 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8061 (mtpt) REVERT: G 3 TYR cc_start: 0.8138 (m-80) cc_final: 0.7864 (m-80) REVERT: G 113 ASP cc_start: 0.7771 (m-30) cc_final: 0.7461 (m-30) REVERT: G 219 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9151 (tp) REVERT: G 234 TYR cc_start: 0.8351 (p90) cc_final: 0.8065 (p90) REVERT: H 42 ASP cc_start: 0.8422 (t70) cc_final: 0.8137 (t70) REVERT: H 65 GLN cc_start: 0.7493 (pp30) cc_final: 0.6911 (pp30) REVERT: H 114 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.9046 (t) outliers start: 88 outliers final: 57 residues processed: 369 average time/residue: 0.1512 time to fit residues: 84.0788 Evaluate side-chains 340 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 152 ILE 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 469 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 516 VAL 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 717 THR 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 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 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 125 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 43 ASN Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 61 THR 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 138 THR 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 83 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 134 ASN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108493 restraints weight = 27609.197| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.18 r_work: 0.3077 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19345 Z= 0.277 Angle : 0.947 17.169 26431 Z= 0.448 Chirality : 0.073 0.927 3005 Planarity : 0.005 0.052 3137 Dihedral : 12.470 144.188 3227 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.71 % Favored : 88.25 % Rotamer: Outliers : 5.46 % Allowed : 15.23 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.17), residues: 2161 helix: -0.30 (0.18), residues: 813 sheet: -2.18 (0.28), residues: 305 loop : -2.64 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 305 TYR 0.033 0.002 TYR G 157 PHE 0.022 0.002 PHE A 246 TRP 0.022 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.28 (19345) covalent geometry : angle 0.94666 / 0.45 (26431) hydrogen bonds : bond 0.04541 / 3.05 ( 729) hydrogen bonds : angle 5.08218 / 3.52 ( 2019) *********************** 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 390 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 291 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7144 (t-100) cc_final: 0.6588 (t-100) REVERT: A 50 ASP cc_start: 0.6746 (p0) cc_final: 0.6255 (t0) REVERT: A 113 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6970 (m) REVERT: A 141 TYR cc_start: 0.7671 (m-10) cc_final: 0.7443 (m-80) REVERT: A 431 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: A 663 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: B 22 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7404 (mtp180) REVERT: B 75 TYR cc_start: 0.8522 (t80) cc_final: 0.8321 (t80) REVERT: B 79 ARG cc_start: 0.8304 (ptp90) cc_final: 0.7590 (ptp-170) REVERT: C 52 ASP cc_start: 0.8378 (m-30) cc_final: 0.8102 (m-30) REVERT: C 60 ASP cc_start: 0.8352 (m-30) cc_final: 0.8082 (m-30) REVERT: C 63 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8434 (mt) REVERT: C 81 ILE cc_start: 0.7038 (tt) cc_final: 0.6631 (tt) REVERT: C 84 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8277 (ttpt) REVERT: D 18 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8926 (pt) REVERT: E 1 MET cc_start: 0.5200 (tpt) cc_final: 0.4777 (mtm) REVERT: E 7 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8417 (ttpp) REVERT: E 67 LYS cc_start: 0.8932 (pttm) cc_final: 0.8299 (ptmm) REVERT: E 107 ASP cc_start: 0.8056 (p0) cc_final: 0.7745 (p0) REVERT: E 163 VAL cc_start: 0.8691 (p) cc_final: 0.8365 (t) REVERT: E 193 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8302 (m) REVERT: F 11 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8480 (mm110) REVERT: F 99 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7425 (ttt-90) REVERT: F 117 TYR cc_start: 0.8834 (m-80) cc_final: 0.8388 (m-10) REVERT: F 143 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8055 (ttp80) REVERT: F 210 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8131 (mtpt) REVERT: G 113 ASP cc_start: 0.7641 (m-30) cc_final: 0.7366 (m-30) REVERT: G 157 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8508 (p90) REVERT: G 219 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9147 (tp) REVERT: H 42 ASP cc_start: 0.8233 (t70) cc_final: 0.7933 (t70) REVERT: H 65 GLN cc_start: 0.7512 (pp30) cc_final: 0.6941 (pp30) REVERT: H 114 VAL cc_start: 0.9318 (OUTLIER) cc_final: 0.8981 (t) outliers start: 99 outliers final: 64 residues processed: 365 average time/residue: 0.1560 time to fit residues: 85.0421 Evaluate side-chains 345 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 270 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 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 368 GLN 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 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 717 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 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 202 THR 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 125 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 36 VAL 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 182 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 61 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 235 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 111 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR 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 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 131 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN D 124 ASN D 134 ASN G 12 ASN G 104 GLN G 134 ASN G 144 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113732 restraints weight = 27391.703| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.95 r_work: 0.3172 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19345 Z= 0.161 Angle : 0.838 15.184 26431 Z= 0.397 Chirality : 0.066 0.945 3005 Planarity : 0.004 0.045 3137 Dihedral : 12.305 141.017 3227 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.48 % Favored : 88.48 % Rotamer: Outliers : 4.58 % Allowed : 17.16 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.17), residues: 2161 helix: 0.07 (0.18), residues: 809 sheet: -2.22 (0.27), residues: 317 loop : -2.55 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 550 TYR 0.033 0.001 TYR G 157 PHE 0.018 0.001 PHE A 348 TRP 0.020 0.002 TRP A 732 HIS 0.007 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (19345) covalent geometry : angle 0.83809 / 0.40 (26431) hydrogen bonds : bond 0.03980 / 2.70 ( 729) hydrogen bonds : angle 4.94133 / 3.44 ( 2019) *********************** 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 375 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 292 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7189 (t-100) cc_final: 0.6664 (t-100) REVERT: A 50 ASP cc_start: 0.6782 (p0) cc_final: 0.6291 (t0) REVERT: A 113 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.7146 (m) REVERT: A 431 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: B 22 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7418 (mtp180) REVERT: B 57 LYS cc_start: 0.8645 (mttt) cc_final: 0.8241 (mttp) REVERT: B 75 TYR cc_start: 0.8497 (t80) cc_final: 0.8243 (t80) REVERT: B 79 ARG cc_start: 0.8368 (ptp90) cc_final: 0.7644 (ptp-170) REVERT: C 52 ASP cc_start: 0.8529 (m-30) cc_final: 0.8219 (m-30) REVERT: C 60 ASP cc_start: 0.8459 (m-30) cc_final: 0.8223 (m-30) REVERT: C 63 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8455 (mt) REVERT: C 81 ILE cc_start: 0.7041 (tt) cc_final: 0.6583 (tt) REVERT: C 84 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8240 (ttpt) REVERT: D 18 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8855 (pt) REVERT: E 1 MET cc_start: 0.5100 (tpt) cc_final: 0.4572 (mtm) REVERT: E 67 LYS cc_start: 0.8983 (pttm) cc_final: 0.8327 (ptmm) REVERT: E 107 ASP cc_start: 0.8088 (p0) cc_final: 0.7823 (p0) REVERT: E 193 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8096 (m) REVERT: F 11 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8493 (mm110) REVERT: F 99 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7539 (ttt-90) REVERT: F 117 TYR cc_start: 0.8896 (m-80) cc_final: 0.8398 (m-10) REVERT: F 143 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8093 (ttp80) REVERT: F 210 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8114 (mtpt) REVERT: G 113 ASP cc_start: 0.7810 (m-30) cc_final: 0.7504 (m-30) REVERT: G 157 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8392 (p90) REVERT: G 219 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9120 (tp) REVERT: H 42 ASP cc_start: 0.8404 (t70) cc_final: 0.8143 (t70) REVERT: H 65 GLN cc_start: 0.7500 (pp30) cc_final: 0.6919 (pp30) REVERT: H 114 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8986 (t) outliers start: 83 outliers final: 47 residues processed: 355 average time/residue: 0.1577 time to fit residues: 83.7325 Evaluate side-chains 332 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 368 GLN 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 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 717 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 LEU 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 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 125 THR 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 36 VAL 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 182 LEU Chi-restraints excluded: chain G residue 12 ASN 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 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 111 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 310 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 180 optimal weight: 0.0770 chunk 80 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118086 restraints weight = 27538.222| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.91 r_work: 0.3247 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4418 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= 0.135 Angle : 0.803 14.925 26431 Z= 0.382 Chirality : 0.063 0.940 3005 Planarity : 0.004 0.042 3137 Dihedral : 11.999 140.215 3227 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.92 % Favored : 89.03 % Rotamer: Outliers : 4.19 % Allowed : 17.88 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.17), residues: 2161 helix: 0.36 (0.18), residues: 804 sheet: -2.11 (0.28), residues: 311 loop : -2.51 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 95 TYR 0.037 0.001 TYR G 157 PHE 0.016 0.001 PHE G 10 TRP 0.017 0.002 TRP A 732 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (19345) covalent geometry : angle 0.80285 / 0.38 (26431) hydrogen bonds : bond 0.03730 / 2.56 ( 729) hydrogen bonds : angle 4.84172 / 3.36 ( 2019) *********************** 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 378 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 302 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7174 (t-100) cc_final: 0.6657 (t-100) REVERT: A 50 ASP cc_start: 0.6796 (p0) cc_final: 0.6326 (t0) REVERT: A 71 TYR cc_start: 0.7745 (m-80) cc_final: 0.6609 (m-80) REVERT: A 113 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.6912 (m) REVERT: A 224 TYR cc_start: 0.5400 (t80) cc_final: 0.4951 (t80) REVERT: A 431 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: A 466 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7423 (t80) REVERT: A 642 ASP cc_start: 0.7573 (t0) cc_final: 0.7357 (t0) REVERT: B 22 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7377 (mtp180) REVERT: B 57 LYS cc_start: 0.8528 (mttt) cc_final: 0.8142 (mttp) REVERT: B 75 TYR cc_start: 0.8411 (t80) cc_final: 0.8179 (t80) REVERT: B 79 ARG cc_start: 0.8355 (ptp90) cc_final: 0.7534 (ptp-170) REVERT: C 52 ASP cc_start: 0.8522 (m-30) cc_final: 0.8202 (m-30) REVERT: C 60 ASP cc_start: 0.8468 (m-30) cc_final: 0.8235 (m-30) REVERT: C 81 ILE cc_start: 0.6926 (tt) cc_final: 0.6481 (tt) REVERT: C 84 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8304 (ttpt) REVERT: E 1 MET cc_start: 0.5177 (tpt) cc_final: 0.4685 (mtm) REVERT: E 67 LYS cc_start: 0.8943 (pttm) cc_final: 0.8331 (ptmm) REVERT: E 107 ASP cc_start: 0.7956 (p0) cc_final: 0.7719 (p0) REVERT: E 212 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6942 (mt) REVERT: F 11 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8412 (mm110) REVERT: F 99 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7491 (ttt-90) REVERT: F 117 TYR cc_start: 0.8825 (m-80) cc_final: 0.8301 (m-10) REVERT: F 143 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8107 (ttp80) REVERT: F 210 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8079 (mtpt) REVERT: G 113 ASP cc_start: 0.7782 (m-30) cc_final: 0.7537 (m-30) REVERT: G 157 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8362 (p90) REVERT: G 195 ASN cc_start: 0.7485 (m-40) cc_final: 0.7168 (t0) REVERT: G 219 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9140 (tp) REVERT: G 258 TYR cc_start: 0.8829 (m-80) cc_final: 0.8607 (m-80) REVERT: H 42 ASP cc_start: 0.8378 (t70) cc_final: 0.8113 (t70) REVERT: H 65 GLN cc_start: 0.7432 (pp30) cc_final: 0.6915 (pp30) REVERT: H 114 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.8978 (t) outliers start: 76 outliers final: 48 residues processed: 356 average time/residue: 0.1535 time to fit residues: 81.6031 Evaluate side-chains 334 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 ASP 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 717 THR 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 58 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 9 SER 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 125 THR 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 E residue 212 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 15 LEU 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 138 THR Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 299 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 37 optimal weight: 0.6980 chunk 117 optimal weight: 0.0070 chunk 209 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119859 restraints weight = 27424.934| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.94 r_work: 0.3272 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19345 Z= 0.134 Angle : 0.801 14.690 26431 Z= 0.381 Chirality : 0.062 0.942 3005 Planarity : 0.004 0.044 3137 Dihedral : 11.850 140.683 3227 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.87 % Favored : 89.08 % Rotamer: Outliers : 3.75 % Allowed : 18.16 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 2161 helix: 0.49 (0.18), residues: 806 sheet: -1.90 (0.28), residues: 319 loop : -2.46 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 550 TYR 0.038 0.001 TYR G 157 PHE 0.022 0.001 PHE E 167 TRP 0.020 0.002 TRP A 732 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (19345) covalent geometry : angle 0.80104 / 0.38 (26431) hydrogen bonds : bond 0.03696 / 2.53 ( 729) hydrogen bonds : angle 4.78622 / 3.30 ( 2019) *********************** 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 363 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7190 (t-100) cc_final: 0.6701 (t-100) REVERT: A 50 ASP cc_start: 0.6818 (p0) cc_final: 0.6350 (t0) REVERT: A 71 TYR cc_start: 0.7736 (m-80) cc_final: 0.6627 (m-80) REVERT: A 224 TYR cc_start: 0.5598 (t80) cc_final: 0.5079 (t80) REVERT: A 431 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: A 463 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7345 (pp30) REVERT: A 466 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 642 ASP cc_start: 0.7458 (t0) cc_final: 0.7212 (t0) REVERT: A 739 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7741 (mtmm) REVERT: B 22 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7434 (mtp180) REVERT: B 79 ARG cc_start: 0.8355 (ptp90) cc_final: 0.7902 (ptp-170) REVERT: C 52 ASP cc_start: 0.8500 (m-30) cc_final: 0.8204 (m-30) REVERT: C 60 ASP cc_start: 0.8531 (m-30) cc_final: 0.8329 (m-30) REVERT: C 81 ILE cc_start: 0.6787 (tt) cc_final: 0.6300 (tt) REVERT: C 84 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8297 (ttpt) REVERT: E 1 MET cc_start: 0.5167 (tpt) cc_final: 0.4676 (mtm) REVERT: E 67 LYS cc_start: 0.8965 (pttm) cc_final: 0.8355 (ptmm) REVERT: E 107 ASP cc_start: 0.7931 (p0) cc_final: 0.7697 (p0) REVERT: F 11 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8354 (mm110) REVERT: F 99 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7496 (ttt-90) REVERT: F 117 TYR cc_start: 0.8767 (m-80) cc_final: 0.8212 (m-80) REVERT: F 143 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8103 (ttp80) REVERT: F 210 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8063 (mtpt) REVERT: G 113 ASP cc_start: 0.7829 (m-30) cc_final: 0.7560 (m-30) REVERT: G 157 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8274 (p90) REVERT: G 219 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9131 (tp) REVERT: G 258 TYR cc_start: 0.8820 (m-80) cc_final: 0.8613 (m-80) REVERT: H 42 ASP cc_start: 0.8369 (t70) cc_final: 0.8102 (t70) REVERT: H 65 GLN cc_start: 0.7318 (pp30) cc_final: 0.6781 (pp30) REVERT: H 114 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8980 (t) REVERT: H 141 MET cc_start: 0.8859 (mtp) cc_final: 0.8659 (mtp) outliers start: 68 outliers final: 51 residues processed: 345 average time/residue: 0.1569 time to fit residues: 80.8705 Evaluate side-chains 332 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 717 THR 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 58 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 86 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 41 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 132 GLU 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 36 VAL Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 158 VAL 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 H residue 15 LEU Chi-restraints excluded: chain H residue 52 GLU 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 138 THR Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 33 optimal weight: 0.0000 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 158 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN H 142 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114433 restraints weight = 27531.151| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.93 r_work: 0.3181 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19345 Z= 0.183 Angle : 0.848 14.994 26431 Z= 0.402 Chirality : 0.066 0.934 3005 Planarity : 0.004 0.080 3137 Dihedral : 11.962 143.490 3227 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.01 % Favored : 88.94 % Rotamer: Outliers : 3.81 % Allowed : 18.38 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.18), residues: 2161 helix: 0.45 (0.18), residues: 812 sheet: -1.70 (0.27), residues: 344 loop : -2.48 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 95 TYR 0.034 0.002 TYR G 157 PHE 0.031 0.001 PHE E 167 TRP 0.022 0.002 TRP A 732 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (19345) covalent geometry : angle 0.84843 / 0.40 (26431) hydrogen bonds : bond 0.03926 / 2.65 ( 729) hydrogen bonds : angle 4.79667 / 3.32 ( 2019) *********************** 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 to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 0.738 Fit side-chains REVERT: A 38 TRP cc_start: 0.7189 (t-100) cc_final: 0.6721 (t-100) REVERT: A 50 ASP cc_start: 0.6842 (p0) cc_final: 0.6333 (t0) REVERT: A 71 TYR cc_start: 0.7736 (m-80) cc_final: 0.6642 (m-80) REVERT: A 224 TYR cc_start: 0.5530 (t80) cc_final: 0.4935 (t80) REVERT: A 463 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7252 (pp30) REVERT: A 466 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7435 (t80) REVERT: A 739 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7802 (mtmm) REVERT: B 22 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7539 (mtp85) REVERT: B 75 TYR cc_start: 0.8539 (t80) cc_final: 0.8287 (t80) REVERT: B 79 ARG cc_start: 0.8315 (ptp90) cc_final: 0.7564 (ptp-170) REVERT: C 52 ASP cc_start: 0.8517 (m-30) cc_final: 0.8216 (m-30) REVERT: C 60 ASP cc_start: 0.8545 (m-30) cc_final: 0.8344 (m-30) REVERT: C 81 ILE cc_start: 0.7059 (tt) cc_final: 0.6618 (tt) REVERT: C 84 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8338 (ttpt) REVERT: E 1 MET cc_start: 0.5258 (tpt) cc_final: 0.4848 (mtt) REVERT: E 67 LYS cc_start: 0.9015 (pttm) cc_final: 0.8384 (ptmm) REVERT: E 107 ASP cc_start: 0.8117 (p0) cc_final: 0.7910 (p0) REVERT: E 193 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8107 (m) REVERT: F 11 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8404 (mm110) REVERT: F 99 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7489 (ttt-90) REVERT: F 117 TYR cc_start: 0.8832 (m-80) cc_final: 0.8312 (m-10) REVERT: F 143 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8172 (ttp80) REVERT: F 177 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8660 (tt) REVERT: F 210 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8109 (mtpt) REVERT: G 113 ASP cc_start: 0.7820 (m-30) cc_final: 0.7609 (m-30) REVERT: G 157 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8519 (p90) REVERT: G 195 ASN cc_start: 0.7601 (m-40) cc_final: 0.7362 (t0) REVERT: G 219 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9127 (tp) REVERT: G 258 TYR cc_start: 0.8947 (m-80) cc_final: 0.8732 (m-80) REVERT: H 42 ASP cc_start: 0.8392 (t70) cc_final: 0.8094 (t70) REVERT: H 65 GLN cc_start: 0.7479 (pp30) cc_final: 0.6959 (pp30) REVERT: H 114 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9027 (t) REVERT: H 142 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8215 (m-40) outliers start: 69 outliers final: 53 residues processed: 329 average time/residue: 0.1483 time to fit residues: 73.7446 Evaluate side-chains 337 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 275 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 717 THR 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 58 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 103 LEU 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 132 GLU 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 36 VAL Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 158 VAL 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 H residue 15 LEU Chi-restraints excluded: chain H residue 52 GLU 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 138 THR Chi-restraints excluded: chain H residue 142 ASN Chi-restraints excluded: chain H residue 225 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 89 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 0.0020 chunk 49 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 0.0170 chunk 155 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 overall best weight: 0.7228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN H 142 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118834 restraints weight = 27304.549| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.86 r_work: 0.3250 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19345 Z= 0.137 Angle : 0.807 14.161 26431 Z= 0.385 Chirality : 0.062 0.920 3005 Planarity : 0.004 0.077 3137 Dihedral : 11.881 140.915 3227 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.83 % Favored : 89.13 % Rotamer: Outliers : 3.31 % Allowed : 19.09 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.18), residues: 2161 helix: 0.52 (0.18), residues: 808 sheet: -1.74 (0.27), residues: 338 loop : -2.38 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 171 TYR 0.037 0.002 TYR G 157 PHE 0.036 0.001 PHE E 167 TRP 0.023 0.002 TRP A 732 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (19345) covalent geometry : angle 0.80730 / 0.39 (26431) hydrogen bonds : bond 0.03688 / 2.53 ( 729) hydrogen bonds : angle 4.79872 / 3.31 ( 2019) ********************** 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 344 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 0.650 Fit side-chains REVERT: A 38 TRP cc_start: 0.7169 (t-100) cc_final: 0.6689 (t-100) REVERT: A 50 ASP cc_start: 0.6794 (p0) cc_final: 0.6282 (t0) REVERT: A 71 TYR cc_start: 0.7729 (m-80) cc_final: 0.6661 (m-80) REVERT: A 224 TYR cc_start: 0.5654 (t80) cc_final: 0.5080 (t80) REVERT: A 389 LEU cc_start: 0.8812 (tt) cc_final: 0.8097 (mp) REVERT: A 463 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7237 (pp30) REVERT: A 466 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7469 (t80) REVERT: A 470 TYR cc_start: 0.5639 (OUTLIER) cc_final: 0.5105 (t80) REVERT: A 642 ASP cc_start: 0.7566 (t0) cc_final: 0.7329 (t0) REVERT: A 739 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7731 (mtmm) REVERT: B 22 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7547 (mtp180) REVERT: B 75 TYR cc_start: 0.8447 (t80) cc_final: 0.8195 (t80) REVERT: B 79 ARG cc_start: 0.8295 (ptp90) cc_final: 0.7589 (ptp-170) REVERT: C 52 ASP cc_start: 0.8472 (m-30) cc_final: 0.8173 (m-30) REVERT: C 60 ASP cc_start: 0.8572 (m-30) cc_final: 0.8367 (m-30) REVERT: C 81 ILE cc_start: 0.6937 (tt) cc_final: 0.6427 (tt) REVERT: C 84 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8292 (ttpt) REVERT: E 1 MET cc_start: 0.5349 (tpt) cc_final: 0.4692 (mtm) REVERT: E 67 LYS cc_start: 0.8993 (pttm) cc_final: 0.8369 (ptmm) REVERT: E 107 ASP cc_start: 0.8079 (p0) cc_final: 0.7877 (p0) REVERT: E 193 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7874 (m) REVERT: F 11 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8370 (mm110) REVERT: F 117 TYR cc_start: 0.8750 (m-80) cc_final: 0.8240 (m-10) REVERT: F 143 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8125 (ttp80) REVERT: F 177 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8591 (tt) REVERT: F 210 LYS cc_start: 0.8557 (mtmm) cc_final: 0.7993 (mtpp) REVERT: G 113 ASP cc_start: 0.7871 (m-30) cc_final: 0.7645 (m-30) REVERT: G 157 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8376 (p90) REVERT: G 219 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9117 (tp) REVERT: H 42 ASP cc_start: 0.8324 (t70) cc_final: 0.8028 (t70) REVERT: H 65 GLN cc_start: 0.7365 (pp30) cc_final: 0.6854 (pp30) REVERT: H 114 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.8992 (t) REVERT: H 142 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7829 (m110) outliers start: 60 outliers final: 44 residues processed: 330 average time/residue: 0.1495 time to fit residues: 74.2174 Evaluate side-chains 333 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 663 TYR Chi-restraints excluded: chain A residue 717 THR 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 58 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 86 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 34 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 132 GLU 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 143 ARG Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 ASN 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 H residue 15 LEU Chi-restraints excluded: chain H residue 52 GLU 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 138 THR Chi-restraints excluded: chain H residue 142 ASN Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 251 GLN Chi-restraints excluded: chain H residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 29 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN G 134 ASN G 246 HIS H 142 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108103 restraints weight = 27675.256| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.01 r_work: 0.3076 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 19345 Z= 0.321 Angle : 0.982 16.743 26431 Z= 0.464 Chirality : 0.075 0.999 3005 Planarity : 0.006 0.084 3137 Dihedral : 12.283 145.962 3227 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.94 % Favored : 88.01 % Rotamer: Outliers : 3.59 % Allowed : 18.82 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.17), residues: 2161 helix: 0.20 (0.18), residues: 822 sheet: -1.66 (0.27), residues: 337 loop : -2.48 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 95 TYR 0.031 0.003 TYR A 490 PHE 0.047 0.002 PHE E 167 TRP 0.025 0.002 TRP A 732 HIS 0.006 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.32 (19345) covalent geometry : angle 0.98196 / 0.46 (26431) hydrogen bonds : bond 0.04579 / 3.04 ( 729) hydrogen bonds : angle 4.96641 / 3.45 ( 2019) =============================================================================== Job complete usr+sys time: 5169.06 seconds wall clock time: 89 minutes 21.73 seconds (5361.73 seconds total)