Starting phenix.real_space_refine on Thu Mar 5 12:55:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whi_21517/03_2026/6whi_21517.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whi_21517/03_2026/6whi_21517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6whi_21517/03_2026/6whi_21517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whi_21517/03_2026/6whi_21517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6whi_21517/03_2026/6whi_21517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whi_21517/03_2026/6whi_21517.map" } resolution = 4.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.004 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 109 5.49 5 S 15 5.16 5 C 13846 2.51 5 N 4080 2.21 5 O 4586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22636 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2187 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 302} Link IDs: {'PTRANS': 22, 'TRANS': 387} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1159 Unresolved non-hydrogen angles: 1483 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 32, 'GLU:plan': 29, 'ARG:plan': 33, 'PHE:plan': 12, 'ASP:plan': 21, 'HIS:plan': 8, 'TRP:plan': 8, 'ASN:plan1': 16, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 732 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2129 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 22, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 10, 'ARG:plan': 14, 'ASN:plan1': 5, 'TRP:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2111 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 10, 'GLU:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "D" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2492 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2500 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2521 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2474 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2484 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 5, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 11, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 18, 'rna3p': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 920 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 159} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 8, 'TYR:plan': 3, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 378 Chain: "I" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 489 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 482 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 174 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' DA:plan': 5, ' DA:plan2': 5, ' DG:plan': 4, ' DG:plan2': 4, ' DC:plan': 3, ' DC:plan2': 3, ' DT:plan': 3} Unresolved non-hydrogen planarities: 160 Chain: "Q" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' DG:plan': 4, ' DG:plan2': 4, ' DC:plan': 3, ' DC:plan2': 3, ' DA:plan': 2, ' DA:plan2': 2, ' DT:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "P" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 114 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' DC:plan': 4, ' DC:plan2': 4, ' DT:plan': 2, ' DG:plan': 3, ' DG:plan2': 3, ' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 105 Chain: "O" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 171 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {' DG:plan': 3, ' DG:plan2': 3, ' DT:plan': 5, ' DC:plan': 4, ' DC:plan2': 4, ' DA:plan': 3, ' DA:plan2': 3} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 5.45, per 1000 atoms: 0.24 Number of scatterers: 22636 At special positions: 0 Unit cell: (138, 139.15, 154.1, 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 15 16.00 P 109 15.00 O 4586 8.00 N 4080 7.00 C 13846 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: 1.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5524 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 41 sheets defined 34.8% alpha, 20.7% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 removed outlier: 4.339A pdb=" N SER A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 removed outlier: 4.510A pdb=" N LYS A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 49 Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.726A pdb=" N ALA A 56 " --> pdb=" O TRP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.879A pdb=" N ALA A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 162 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.878A pdb=" N PHE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 314 through 342 removed outlier: 3.737A pdb=" N ARG A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.975A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.909A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.596A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 181 removed outlier: 3.888A pdb=" N ARG B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.772A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.029A pdb=" N ASP C 53 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER C 55 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 148 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 208 through 224 Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.779A pdb=" N ALA C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.815A pdb=" N SER C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.507A pdb=" N ARG D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.887A pdb=" N ALA D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.738A pdb=" N SER D 306 " --> pdb=" O PRO D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 49 through 54 removed outlier: 4.150A pdb=" N ASP E 53 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 Processing helix chain 'E' and resid 130 through 148 removed outlier: 3.560A pdb=" N ARG E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 163 Processing helix chain 'E' and resid 208 through 224 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.698A pdb=" N ALA E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.074A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.153A pdb=" N ASP F 53 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 91 Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.513A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 208 through 224 Processing helix chain 'F' and resid 275 through 284 removed outlier: 3.692A pdb=" N ALA F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.735A pdb=" N SER F 306 " --> pdb=" O PRO F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 49 through 54 removed outlier: 4.161A pdb=" N ASP G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.568A pdb=" N ASP G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 removed outlier: 3.585A pdb=" N ARG G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 208 through 224 Processing helix chain 'G' and resid 275 through 284 removed outlier: 3.603A pdb=" N ALA G 282 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 306 removed outlier: 3.910A pdb=" N SER G 306 " --> pdb=" O PRO G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 333 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 48 through 53 removed outlier: 4.526A pdb=" N ASP H 53 " --> pdb=" O TRP H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'H' and resid 208 through 224 Processing helix chain 'H' and resid 275 through 284 removed outlier: 3.573A pdb=" N ALA H 282 " --> pdb=" O LYS H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 306 removed outlier: 3.715A pdb=" N SER H 306 " --> pdb=" O PRO H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 333 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'L' and resid 16 through 33 removed outlier: 3.601A pdb=" N GLN L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 73 removed outlier: 3.752A pdb=" N ALA L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 121 removed outlier: 3.716A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 131 Processing helix chain 'L' and resid 132 through 136 removed outlier: 3.914A pdb=" N ALA L 136 " --> pdb=" O ASP L 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'J' and resid 26 through 37 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.863A pdb=" N ASP A 107 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.618A pdb=" N ALA A 95 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 3.554A pdb=" N SER B 143 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 251 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 190 removed outlier: 6.769A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.914A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 240 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.665A pdb=" N TRP B 29 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 306 through 307 Processing sheet with id=AA9, first strand: chain 'C' and resid 127 through 128 removed outlier: 3.956A pdb=" N ALA C 127 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 31 " --> pdb=" O PHE C 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.636A pdb=" N ASP C 38 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG C 117 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189 removed outlier: 4.581A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 272 " --> pdb=" O MET C 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.770A pdb=" N THR C 264 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 128 removed outlier: 3.807A pdb=" N ALA D 127 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 32 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 31 " --> pdb=" O PHE D 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.728A pdb=" N ARG D 117 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 118 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 188 through 189 removed outlier: 4.538A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 118 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA D 272 " --> pdb=" O MET D 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 64 through 70 removed outlier: 3.554A pdb=" N ARG D 64 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER D 262 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR D 97 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR D 264 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP D 99 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 127 through 128 removed outlier: 4.140A pdb=" N ALA E 127 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 32 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU E 31 " --> pdb=" O PHE E 355 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.763A pdb=" N ARG E 117 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.763A pdb=" N ARG E 117 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA E 272 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 64 through 69 removed outlier: 3.508A pdb=" N VAL E 98 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 64 through 69 removed outlier: 3.508A pdb=" N VAL E 98 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN E 260 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.874A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 32 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE F 33 " --> pdb=" O GLY F 353 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY F 353 " --> pdb=" O PHE F 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.645A pdb=" N ASP F 38 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 117 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 231 " --> pdb=" O ASN F 182 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.645A pdb=" N ASP F 38 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 117 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA F 272 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 64 through 70 removed outlier: 3.580A pdb=" N GLN F 96 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 248 through 249 removed outlier: 3.796A pdb=" N THR F 264 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 128 removed outlier: 3.843A pdb=" N ALA G 127 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 32 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU G 31 " --> pdb=" O PHE G 355 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.703A pdb=" N ASP G 38 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU G 231 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 188 through 189 removed outlier: 3.587A pdb=" N GLU G 231 " --> pdb=" O ASN G 182 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.628A pdb=" N VAL G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.628A pdb=" N VAL G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR G 97 " --> pdb=" O SER G 262 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR G 264 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP G 99 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR G 264 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.817A pdb=" N ALA H 127 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 32 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU H 31 " --> pdb=" O PHE H 355 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.531A pdb=" N ASP H 38 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG H 117 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL H 179 " --> pdb=" O PHE H 195 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.531A pdb=" N ASP H 38 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG H 117 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA H 272 " --> pdb=" O MET H 44 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 64 through 70 removed outlier: 4.884A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 41 through 43 removed outlier: 3.823A pdb=" N ALA L 62 " --> pdb=" O HIS L 3 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS L 3 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AE2, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=AE3, first strand: chain 'L' and resid 146 through 148 removed outlier: 5.315A pdb=" N SER L 148 " --> pdb=" O GLN L 153 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN L 153 " --> pdb=" O SER L 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 20 through 21 removed outlier: 3.638A pdb=" N VAL I 20 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER I 49 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP I 54 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 20 through 21 removed outlier: 6.529A pdb=" N SER J 49 " --> pdb=" O TRP J 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP J 54 " --> pdb=" O SER J 49 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3686 1.31 - 1.43: 6203 1.43 - 1.56: 13062 1.56 - 1.68: 214 1.68 - 1.80: 22 Bond restraints: 23187 Sorted by residual: bond pdb=" C ALA E 300 " pdb=" N VAL E 301 " ideal model delta sigma weight residual 1.333 1.260 0.073 1.20e-02 6.94e+03 3.66e+01 bond pdb=" C ARG E 315 " pdb=" O ARG E 315 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.26e-02 6.30e+03 1.88e+01 bond pdb=" N PRO A 269 " pdb=" CD PRO A 269 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta sigma weight residual 1.467 1.420 0.047 1.21e-02 6.83e+03 1.49e+01 bond pdb=" CA VAL E 301 " pdb=" CB VAL E 301 " ideal model delta sigma weight residual 1.536 1.491 0.045 1.16e-02 7.43e+03 1.48e+01 ... (remaining 23182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 31812 3.74 - 7.48: 200 7.48 - 11.22: 10 11.22 - 14.96: 6 14.96 - 18.70: 2 Bond angle restraints: 32030 Sorted by residual: angle pdb=" N LEU A 94 " pdb=" CA LEU A 94 " pdb=" C LEU A 94 " ideal model delta sigma weight residual 109.07 90.37 18.70 1.52e+00 4.33e-01 1.51e+02 angle pdb=" N TYR A 187 " pdb=" CA TYR A 187 " pdb=" C TYR A 187 " ideal model delta sigma weight residual 110.53 124.16 -13.63 1.32e+00 5.74e-01 1.07e+02 angle pdb=" N LEU A 104 " pdb=" CA LEU A 104 " pdb=" C LEU A 104 " ideal model delta sigma weight residual 109.15 95.33 13.82 1.44e+00 4.82e-01 9.21e+01 angle pdb=" C ALA E 300 " pdb=" N VAL E 301 " pdb=" CA VAL E 301 " ideal model delta sigma weight residual 120.98 108.38 12.60 1.36e+00 5.41e-01 8.58e+01 angle pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" CD PRO A 266 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.34e+01 ... (remaining 32025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 13315 21.12 - 42.24: 384 42.24 - 63.37: 196 63.37 - 84.49: 44 84.49 - 105.61: 5 Dihedral angle restraints: 13944 sinusoidal: 5409 harmonic: 8535 Sorted by residual: dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 102.74 97.26 1 1.50e+01 4.44e-03 4.81e+01 dihedral pdb=" O4' U M 2 " pdb=" C1' U M 2 " pdb=" N1 U M 2 " pdb=" C2 U M 2 " ideal model delta sinusoidal sigma weight residual -128.00 -38.81 -89.19 1 1.70e+01 3.46e-03 3.27e+01 dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual -160.00 -94.55 -65.45 1 1.50e+01 4.44e-03 2.49e+01 ... (remaining 13941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3652 0.111 - 0.223: 179 0.223 - 0.334: 19 0.334 - 0.445: 2 0.445 - 0.557: 1 Chirality restraints: 3853 Sorted by residual: chirality pdb=" C3' U M 10 " pdb=" C4' U M 10 " pdb=" O3' U M 10 " pdb=" C2' U M 10 " both_signs ideal model delta sigma weight residual False -2.48 -1.92 -0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" CA ASP H 256 " pdb=" N ASP H 256 " pdb=" C ASP H 256 " pdb=" CB ASP H 256 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C1' G M 26 " pdb=" O4' G M 26 " pdb=" C2' G M 26 " pdb=" N9 G M 26 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 3850 not shown) Planarity restraints: 3906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 265 " -0.123 5.00e-02 4.00e+02 1.74e-01 4.83e+01 pdb=" N PRO A 266 " 0.300 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U M 10 " -0.045 2.00e-02 2.50e+03 3.57e-02 2.86e+01 pdb=" N1 U M 10 " 0.088 2.00e-02 2.50e+03 pdb=" C2 U M 10 " -0.037 2.00e-02 2.50e+03 pdb=" O2 U M 10 " 0.010 2.00e-02 2.50e+03 pdb=" N3 U M 10 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U M 10 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U M 10 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U M 10 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U M 10 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 301 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.53e+01 pdb=" C VAL E 301 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL E 301 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU E 302 " 0.023 2.00e-02 2.50e+03 ... (remaining 3903 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 217 2.52 - 3.12: 17764 3.12 - 3.71: 33199 3.71 - 4.31: 44959 4.31 - 4.90: 76228 Nonbonded interactions: 172367 Sorted by model distance: nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 1.927 3.040 nonbonded pdb=" OG SER B 143 " pdb=" OD2 ASP H 38 " model vdw 1.957 3.040 nonbonded pdb=" O ARG G 69 " pdb=" O2' G M 19 " model vdw 1.962 3.040 nonbonded pdb=" O2' G M 18 " pdb=" O4' G M 19 " model vdw 1.971 3.040 nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 1.987 3.040 ... (remaining 172362 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 'C' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 190 or (resid 191 through 192 and \ (name N or name CA or name C or name O or name CB )) or resid 193 through 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 8 through 285 or (resid 286 and (name N or name CA or name C or name O or name C \ B )) or resid 287 through 295 or (resid 296 and (name N or name CA or name C or \ name O or name CB )) or resid 297 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 356)) selection = (chain 'D' and (resid 25 through 50 or (resid 51 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 and (na \ me N or name CA or name C or name O or name CB )) or resid 65 through 66 or resi \ d 98 through 104 or (resid 105 through 107 and (name N or name CA or name C or n \ ame O or name CB )) or resid 108 through 145 or (resid 146 through 147 and (name \ N or name CA or name C or name O or name CB )) or resid 148 through 151 or (res \ id 152 and (name N or name CA or name C or name O or name CB )) or resid 153 thr \ ough 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) \ or resid 170 through 174 or (resid 175 through 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 184 or (resid 185 through 186 a \ nd (name N or name CA or name C or name O or name CB )) or resid 187 or (resid 1 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 189 through \ 190 or (resid 191 through 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 195 or (resid 196 through 199 and (name N or name C \ A or name C or name O or name CB )) or resid 200 through 201 or (resid 202 throu \ gh 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 209 or (resid 210 and (name N or name CA or name C or name \ O or name CB )) or resid 211 through 226 or (resid 227 and (name N or name CA or \ name C or name O or name CB )) or resid 228 through 239 or (resid 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 249 or (res \ id 250 and (name N or name CA or name C or name O or name CB )) or resid 263 thr \ ough 268 or (resid 269 through 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 through 303 or (resid 304 and (name N or name CA or nam \ e C or name O or name CB )) or resid 305 through 311 or (resid 312 through 313 a \ nd (name N or name CA or name C or name O or name CB )) or resid 314 through 317 \ or (resid 318 and (name N or name CA or name C or name O or name CB )) or resid \ 319 or (resid 320 through 322 and (name N or name CA or name C or name O or nam \ e CB )) or resid 323 through 339 or (resid 340 and (name N or name CA or name C \ or name O or name CB )) or resid 341 through 356)) selection = (chain 'E' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 295 or (resid 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 311 or (resid 312 \ through 313 and (name N or name CA or name C or name O or name CB )) or resid 31 \ 4 through 317 or (resid 318 and (name N or name CA or name C or name O or name C \ B )) or resid 319 or (resid 320 through 322 and (name N or name CA or name C or \ name O or name CB )) or resid 323 through 339 or (resid 340 and (name N or name \ CA or name C or name O or name CB )) or resid 341 through 356)) selection = (chain 'F' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 201 or (re \ sid 202 through 204 and (name N or name CA or name C or name O or name CB )) or \ resid 205 or (resid 206 through 207 and (name N or name CA or name C or name O o \ r name CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 239 or (resid \ 240 and (name N or name CA or name C or name O or name CB )) or resid 241 throug \ h 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 268 or (resid 269 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 295 or (resid 296 and (name N or n \ ame CA or name C or name O or name CB )) or resid 297 through 303 or (resid 304 \ and (name N or name CA or name C or name O or name CB )) or resid 305 through 31 \ 1 or (resid 312 through 313 and (name N or name CA or name C or name O or name C \ B )) or resid 314 through 317 or (resid 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 or (resid 320 through 322 and (name N or name \ CA or name C or name O or name CB )) or resid 323 through 339 or (resid 340 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 356)) selection = (chain 'G' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 190 or (resid 191 through 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 195 or (resid 196 through 199 and (name N \ or name CA or name C or name O or name CB )) or resid 200 through 201 or (resid \ 202 through 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 or (resid 206 through 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 226 or (resid 227 and (name N or n \ ame CA or name C or name O or name CB )) or resid 228 through 239 or (resid 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 9 or (resid 250 and (name N or name CA or name C or name O or name CB )) or resi \ d 263 through 268 or (resid 269 through 273 and (name N or name CA or name C or \ name O or name CB )) or resid 274 through 285 or (resid 286 and (name N or name \ CA or name C or name O or name CB )) or resid 287 through 295 or (resid 296 and \ (name N or name CA or name C or name O or name CB )) or resid 297 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 5 through 311 or (resid 312 through 313 and (name N or name CA or name C or name \ O or name CB )) or resid 314 through 317 or (resid 318 and (name N or name CA o \ r name C or name O or name CB )) or resid 319 or (resid 320 through 322 and (nam \ e N or name CA or name C or name O or name CB )) or resid 323 through 339 or (re \ sid 340 and (name N or name CA or name C or name O or name CB )) or resid 341 th \ rough 356)) selection = (chain 'H' and (resid 25 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 50 or (resid 51 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 63 or (res \ id 64 and (name N or name CA or name C or name O or name CB )) or resid 65 throu \ gh 66 or resid 98 through 104 or (resid 105 through 107 and (name N or name CA o \ r name C or name O or name CB )) or resid 108 through 145 or (resid 146 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 throug \ h 151 or (resid 152 and (name N or name CA or name C or name O or name CB )) or \ resid 153 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 174 or (resid 175 through 176 and (name N or n \ ame CA or name C or name O or name CB )) or resid 177 through 184 or (resid 185 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 or (resid 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 195 or (resid 196 through 199 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 201 or (resid 202 through 204 and (nam \ e N or name CA or name C or name O or name CB )) or resid 205 or (resid 206 thro \ ugh 207 and (name N or name CA or name C or name O or name CB )) or resid 208 th \ rough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 211 through 239 or (resid 240 and (name N or name CA or name C or name \ O or name CB )) or resid 241 through 249 or (resid 250 and (name N or name CA o \ r name C or name O or name CB )) or resid 263 through 268 or (resid 269 through \ 273 and (name N or name CA or name C or name O or name CB )) or resid 274 throug \ h 303 or (resid 304 and (name N or name CA or name C or name O or name CB )) or \ resid 305 through 311 or (resid 312 through 313 and (name N or name CA or name C \ or name O or name CB )) or resid 314 through 317 or (resid 318 and (name N or n \ ame CA or name C or name O or name CB )) or resid 319 through 320 or (resid 321 \ through 322 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 3 through 339 or (resid 340 and (name N or name CA or name C or name O or name C \ B )) or resid 341 through 356)) } ncs_group { reference = (chain 'I' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 36 or (resid 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 through 52 or (resid 53 and (n \ ame N or name CA or name C or name O or name CB )) or resid 54 through 58 or (re \ sid 59 through 60 and (name N or name CA or name C or name O or name CB )) or re \ sid 61 through 66)) selection = (chain 'J' and (resid 3 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 47 or (resid 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 66)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.380 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.005 0.073 23187 Z= 0.293 Angle : 0.947 18.698 32030 Z= 0.625 Chirality : 0.056 0.557 3853 Planarity : 0.005 0.174 3906 Dihedral : 13.261 105.611 8420 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.63 (0.14), residues: 2930 helix: 0.67 (0.18), residues: 891 sheet: -1.10 (0.22), residues: 415 loop : -2.19 (0.13), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 113 TYR 0.019 0.002 TYR D 290 PHE 0.028 0.002 PHE E 166 TRP 0.037 0.002 TRP G 193 HIS 0.008 0.002 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00534 (23187) covalent geometry : angle 0.94687 (32030) hydrogen bonds : bond 0.20601 ( 962) hydrogen bonds : angle 7.81483 ( 2835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 LEU cc_start: 0.5592 (mt) cc_final: 0.5030 (pp) REVERT: B 125 GLU cc_start: 0.7099 (tp30) cc_final: 0.6670 (tm-30) REVERT: C 168 TRP cc_start: 0.8171 (m100) cc_final: 0.7893 (m100) REVERT: D 109 THR cc_start: 0.9049 (m) cc_final: 0.8310 (p) REVERT: D 143 THR cc_start: 0.8397 (m) cc_final: 0.8084 (m) REVERT: D 348 ASN cc_start: 0.8426 (t0) cc_final: 0.8007 (t0) REVERT: E 76 LEU cc_start: 0.7500 (mp) cc_final: 0.7080 (mt) REVERT: E 208 ASP cc_start: 0.6778 (t0) cc_final: 0.6427 (m-30) REVERT: E 287 ASP cc_start: 0.7076 (t0) cc_final: 0.6493 (t0) REVERT: E 299 ILE cc_start: 0.9125 (mt) cc_final: 0.8837 (mt) REVERT: F 194 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7498 (mtp180) REVERT: F 321 LEU cc_start: 0.7250 (mt) cc_final: 0.6928 (mt) REVERT: G 102 ASN cc_start: 0.8567 (m-40) cc_final: 0.8167 (m-40) REVERT: G 233 VAL cc_start: 0.9337 (t) cc_final: 0.9129 (m) REVERT: G 245 PHE cc_start: 0.8741 (m-80) cc_final: 0.8291 (m-80) REVERT: G 354 VAL cc_start: 0.8756 (t) cc_final: 0.8544 (p) REVERT: H 175 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7562 (mt-10) REVERT: H 287 ASP cc_start: 0.8265 (t0) cc_final: 0.7954 (t0) REVERT: H 290 TYR cc_start: 0.5689 (p90) cc_final: 0.5123 (p90) REVERT: H 322 ASP cc_start: 0.7013 (t0) cc_final: 0.6559 (t70) REVERT: I 54 TRP cc_start: 0.7635 (m-10) cc_final: 0.7386 (m-10) REVERT: J 49 SER cc_start: 0.8762 (p) cc_final: 0.8457 (m) REVERT: J 64 TRP cc_start: 0.8789 (m100) cc_final: 0.7680 (m100) outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.1656 time to fit residues: 159.1044 Evaluate side-chains 321 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 230 HIS B 45 GLN B 195 GLN C 148 GLN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 227 HIS D 310 GLN E 242 GLN E 348 ASN F 170 ASN F 319 GLN G 348 ASN ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN J 14 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.172559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142960 restraints weight = 39121.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145372 restraints weight = 24715.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147037 restraints weight = 17279.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.148186 restraints weight = 13121.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148782 restraints weight = 10778.010| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23187 Z= 0.125 Angle : 0.549 10.859 32030 Z= 0.292 Chirality : 0.040 0.341 3853 Planarity : 0.004 0.072 3906 Dihedral : 15.072 123.986 4592 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.39 (0.15), residues: 2930 helix: 1.72 (0.18), residues: 920 sheet: -0.41 (0.20), residues: 474 loop : -1.51 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 189 TYR 0.017 0.002 TYR E 290 PHE 0.018 0.002 PHE D 245 TRP 0.032 0.002 TRP A 228 HIS 0.009 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00266 (23187) covalent geometry : angle 0.54942 (32030) hydrogen bonds : bond 0.03476 ( 962) hydrogen bonds : angle 5.04590 ( 2835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8236 (pp) cc_final: 0.7821 (mt) REVERT: A 193 LEU cc_start: 0.8715 (mt) cc_final: 0.8511 (mt) REVERT: B 188 SER cc_start: 0.8906 (t) cc_final: 0.8432 (t) REVERT: C 163 ASN cc_start: 0.8465 (p0) cc_final: 0.8041 (p0) REVERT: C 342 GLN cc_start: 0.8821 (mt0) cc_final: 0.8412 (mt0) REVERT: D 86 LEU cc_start: 0.8142 (mt) cc_final: 0.7921 (mt) REVERT: D 109 THR cc_start: 0.9117 (m) cc_final: 0.8373 (p) REVERT: E 49 TRP cc_start: 0.9054 (t-100) cc_final: 0.8493 (t-100) REVERT: E 62 THR cc_start: 0.8652 (p) cc_final: 0.8447 (t) REVERT: E 130 ASP cc_start: 0.7992 (t0) cc_final: 0.7692 (m-30) REVERT: E 245 PHE cc_start: 0.7790 (m-10) cc_final: 0.7389 (m-10) REVERT: E 270 ASP cc_start: 0.8261 (t0) cc_final: 0.8048 (t70) REVERT: F 78 THR cc_start: 0.7654 (p) cc_final: 0.7410 (p) REVERT: F 90 ILE cc_start: 0.8725 (pt) cc_final: 0.8277 (mt) REVERT: F 146 ASN cc_start: 0.8201 (t0) cc_final: 0.7987 (t0) REVERT: F 169 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7414 (ttt180) REVERT: F 225 SER cc_start: 0.8505 (m) cc_final: 0.8104 (p) REVERT: F 245 PHE cc_start: 0.8519 (m-80) cc_final: 0.8037 (m-80) REVERT: G 278 LYS cc_start: 0.8691 (tptp) cc_final: 0.8417 (tptm) REVERT: G 287 ASP cc_start: 0.8224 (t0) cc_final: 0.7797 (t0) REVERT: G 315 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7723 (ttp-170) REVERT: G 354 VAL cc_start: 0.8850 (t) cc_final: 0.8648 (p) REVERT: H 330 TRP cc_start: 0.8409 (t60) cc_final: 0.7618 (t60) REVERT: I 54 TRP cc_start: 0.8014 (m-10) cc_final: 0.7746 (m-10) REVERT: I 57 TYR cc_start: 0.8928 (p90) cc_final: 0.8699 (p90) REVERT: J 44 VAL cc_start: 0.9399 (m) cc_final: 0.9107 (p) outliers start: 1 outliers final: 0 residues processed: 462 average time/residue: 0.1410 time to fit residues: 102.6774 Evaluate side-chains 299 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 171 optimal weight: 3.9990 chunk 277 optimal weight: 30.0000 chunk 284 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 273 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 45 GLN B 104 HIS D 94 ASN D 248 GLN D 343 HIS ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN E 242 GLN ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 102 ASN F 170 ASN F 281 ASN F 310 GLN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** J 14 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 = 0.3780 r_free = 0.3780 target = 0.152534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120608 restraints weight = 39874.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122782 restraints weight = 26248.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124360 restraints weight = 19136.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125297 restraints weight = 15045.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126169 restraints weight = 12676.601| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23187 Z= 0.209 Angle : 0.617 11.137 32030 Z= 0.330 Chirality : 0.042 0.177 3853 Planarity : 0.005 0.120 3906 Dihedral : 15.206 123.980 4592 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.31 (0.15), residues: 2930 helix: 1.63 (0.18), residues: 930 sheet: 0.05 (0.21), residues: 486 loop : -1.54 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 237 TYR 0.023 0.002 TYR H 344 PHE 0.026 0.002 PHE D 245 TRP 0.027 0.002 TRP H 49 HIS 0.013 0.002 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00468 (23187) covalent geometry : angle 0.61734 (32030) hydrogen bonds : bond 0.03970 ( 962) hydrogen bonds : angle 4.89666 ( 2835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7662 (tm-30) REVERT: C 245 PHE cc_start: 0.8203 (m-80) cc_final: 0.7880 (m-10) REVERT: D 41 ASP cc_start: 0.8503 (m-30) cc_final: 0.8147 (p0) REVERT: D 69 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7753 (ttt180) REVERT: D 242 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7987 (tp40) REVERT: D 321 LEU cc_start: 0.8178 (mt) cc_final: 0.7727 (mp) REVERT: E 49 TRP cc_start: 0.9173 (t-100) cc_final: 0.8653 (t-100) REVERT: E 62 THR cc_start: 0.8716 (p) cc_final: 0.8343 (t) REVERT: E 189 VAL cc_start: 0.9354 (t) cc_final: 0.9002 (m) REVERT: F 102 ASN cc_start: 0.8946 (m110) cc_final: 0.8470 (m-40) REVERT: F 225 SER cc_start: 0.8925 (m) cc_final: 0.8372 (p) REVERT: F 245 PHE cc_start: 0.8866 (m-80) cc_final: 0.8608 (m-80) REVERT: F 277 GLN cc_start: 0.8968 (pm20) cc_final: 0.8710 (pm20) REVERT: G 195 PHE cc_start: 0.8759 (m-10) cc_final: 0.8517 (m-10) REVERT: G 348 ASN cc_start: 0.8799 (t0) cc_final: 0.8566 (t0) REVERT: H 269 ARG cc_start: 0.7760 (mmt90) cc_final: 0.7302 (mtm-85) REVERT: H 322 ASP cc_start: 0.7872 (t0) cc_final: 0.7657 (t0) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.1439 time to fit residues: 89.1134 Evaluate side-chains 259 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 142 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 166 optimal weight: 6.9990 chunk 280 optimal weight: 50.0000 chunk 262 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 3 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A 237 ASN B 45 GLN B 282 ASN B 305 HIS D 170 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN H 102 ASN ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115669 restraints weight = 40437.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.115045 restraints weight = 34223.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115418 restraints weight = 31290.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116410 restraints weight = 25927.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116928 restraints weight = 21631.251| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 23187 Z= 0.296 Angle : 0.678 10.392 32030 Z= 0.365 Chirality : 0.043 0.271 3853 Planarity : 0.005 0.054 3906 Dihedral : 15.314 122.073 4592 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.64 (0.15), residues: 2930 helix: 1.23 (0.17), residues: 932 sheet: 0.03 (0.22), residues: 492 loop : -1.72 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 169 TYR 0.032 0.003 TYR F 290 PHE 0.030 0.002 PHE D 245 TRP 0.034 0.003 TRP B 316 HIS 0.010 0.002 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00661 (23187) covalent geometry : angle 0.67761 (32030) hydrogen bonds : bond 0.04430 ( 962) hydrogen bonds : angle 5.20980 ( 2835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9530 (m-40) cc_final: 0.9220 (m110) REVERT: B 33 SER cc_start: 0.9275 (p) cc_final: 0.8948 (p) REVERT: B 132 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7829 (tm-30) REVERT: B 288 GLU cc_start: 0.7355 (tt0) cc_final: 0.6908 (tt0) REVERT: C 44 MET cc_start: 0.8536 (mtm) cc_final: 0.8256 (mtm) REVERT: C 58 TRP cc_start: 0.8718 (m-10) cc_final: 0.8114 (m-10) REVERT: C 163 ASN cc_start: 0.8629 (p0) cc_final: 0.8095 (p0) REVERT: C 216 GLU cc_start: 0.8584 (pp20) cc_final: 0.8337 (pp20) REVERT: C 310 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8242 (tm-30) REVERT: D 74 ASN cc_start: 0.9070 (p0) cc_final: 0.8723 (p0) REVERT: D 76 LEU cc_start: 0.8230 (tp) cc_final: 0.8000 (tp) REVERT: D 91 GLN cc_start: 0.8190 (mm110) cc_final: 0.7702 (mm110) REVERT: D 206 LYS cc_start: 0.8688 (mppt) cc_final: 0.8247 (mttt) REVERT: D 242 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8214 (mm-40) REVERT: D 314 TYR cc_start: 0.8945 (m-80) cc_final: 0.8574 (m-10) REVERT: D 321 LEU cc_start: 0.8673 (mt) cc_final: 0.8229 (mp) REVERT: E 62 THR cc_start: 0.8882 (p) cc_final: 0.8506 (t) REVERT: E 124 THR cc_start: 0.9499 (m) cc_final: 0.9124 (p) REVERT: E 212 ASP cc_start: 0.8545 (m-30) cc_final: 0.8081 (t0) REVERT: E 242 GLN cc_start: 0.9258 (mm-40) cc_final: 0.9022 (mm-40) REVERT: E 245 PHE cc_start: 0.8768 (m-10) cc_final: 0.8450 (m-10) REVERT: E 277 GLN cc_start: 0.9069 (pm20) cc_final: 0.7966 (pp30) REVERT: E 315 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8349 (mtt-85) REVERT: F 277 GLN cc_start: 0.9002 (pm20) cc_final: 0.8692 (pm20) REVERT: G 94 ASN cc_start: 0.8429 (p0) cc_final: 0.8108 (p0) REVERT: G 109 THR cc_start: 0.9058 (m) cc_final: 0.8479 (p) REVERT: H 49 TRP cc_start: 0.8816 (t-100) cc_final: 0.8590 (t60) REVERT: H 102 ASN cc_start: 0.8140 (m110) cc_final: 0.7493 (m-40) REVERT: H 202 LEU cc_start: 0.8757 (tp) cc_final: 0.8548 (tt) REVERT: H 269 ARG cc_start: 0.7865 (mmt90) cc_final: 0.7353 (mtm-85) REVERT: H 312 LYS cc_start: 0.8308 (ptmt) cc_final: 0.8051 (ptmt) REVERT: H 322 ASP cc_start: 0.8276 (t0) cc_final: 0.8020 (t0) REVERT: I 6 ILE cc_start: 0.9074 (mt) cc_final: 0.8521 (tp) REVERT: I 43 THR cc_start: 0.9648 (p) cc_final: 0.9295 (m) REVERT: I 54 TRP cc_start: 0.9207 (m-10) cc_final: 0.8895 (m-10) REVERT: I 65 ILE cc_start: 0.9500 (mt) cc_final: 0.9240 (mm) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1321 time to fit residues: 72.5911 Evaluate side-chains 241 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 272 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 55 optimal weight: 0.0770 chunk 257 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 50.0000 chunk 126 optimal weight: 0.0470 chunk 267 optimal weight: 30.0000 chunk 250 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS C 227 HIS C 281 ASN C 348 ASN D 94 ASN D 248 GLN D 281 ASN D 348 ASN E 91 GLN E 310 GLN E 348 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN G 148 GLN G 348 ASN ** J 14 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 = 0.3771 r_free = 0.3771 target = 0.151737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123195 restraints weight = 39528.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123595 restraints weight = 28320.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123741 restraints weight = 25356.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124759 restraints weight = 22645.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124880 restraints weight = 18412.040| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23187 Z= 0.117 Angle : 0.512 9.782 32030 Z= 0.272 Chirality : 0.038 0.211 3853 Planarity : 0.003 0.039 3906 Dihedral : 15.058 119.436 4592 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.11 % Allowed : 1.49 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.22 (0.15), residues: 2930 helix: 1.70 (0.18), residues: 932 sheet: 0.20 (0.23), residues: 513 loop : -1.56 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 191 TYR 0.015 0.002 TYR D 290 PHE 0.013 0.001 PHE G 166 TRP 0.036 0.001 TRP A 228 HIS 0.007 0.001 HIS E 227 Details of bonding type rmsd covalent geometry : bond 0.00251 (23187) covalent geometry : angle 0.51167 (32030) hydrogen bonds : bond 0.03072 ( 962) hydrogen bonds : angle 4.54810 ( 2835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9471 (m-40) cc_final: 0.9110 (m110) REVERT: B 54 ILE cc_start: 0.7460 (mt) cc_final: 0.6874 (mt) REVERT: B 132 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7827 (tm-30) REVERT: B 288 GLU cc_start: 0.7400 (tt0) cc_final: 0.6871 (tt0) REVERT: C 163 ASN cc_start: 0.8492 (p0) cc_final: 0.7998 (p0) REVERT: C 216 GLU cc_start: 0.8572 (pp20) cc_final: 0.8303 (pp20) REVERT: C 238 ILE cc_start: 0.9236 (mm) cc_final: 0.8902 (tt) REVERT: C 249 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7137 (tp30) REVERT: C 348 ASN cc_start: 0.8981 (t160) cc_final: 0.8689 (t0) REVERT: D 74 ASN cc_start: 0.8947 (p0) cc_final: 0.8668 (p0) REVERT: D 206 LYS cc_start: 0.8681 (mppt) cc_final: 0.8243 (mttt) REVERT: D 242 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8086 (mm-40) REVERT: D 302 GLU cc_start: 0.8274 (tp30) cc_final: 0.8003 (tp30) REVERT: D 314 TYR cc_start: 0.8841 (m-80) cc_final: 0.8415 (m-10) REVERT: D 321 LEU cc_start: 0.8100 (mt) cc_final: 0.7586 (mp) REVERT: E 62 THR cc_start: 0.8844 (p) cc_final: 0.8456 (t) REVERT: E 109 THR cc_start: 0.9392 (m) cc_final: 0.8788 (p) REVERT: E 124 THR cc_start: 0.9489 (m) cc_final: 0.9103 (p) REVERT: E 212 ASP cc_start: 0.8512 (m-30) cc_final: 0.8224 (t0) REVERT: E 354 VAL cc_start: 0.9186 (t) cc_final: 0.8946 (p) REVERT: F 102 ASN cc_start: 0.9026 (m110) cc_final: 0.8529 (m-40) REVERT: F 189 VAL cc_start: 0.9521 (t) cc_final: 0.9179 (m) REVERT: F 299 ILE cc_start: 0.8207 (pt) cc_final: 0.7981 (pt) REVERT: G 94 ASN cc_start: 0.8467 (p0) cc_final: 0.8104 (p0) REVERT: G 105 SER cc_start: 0.7963 (t) cc_final: 0.7749 (p) REVERT: G 109 THR cc_start: 0.8875 (m) cc_final: 0.8354 (p) REVERT: H 102 ASN cc_start: 0.8161 (m110) cc_final: 0.7881 (m-40) REVERT: H 269 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7238 (mtm-85) REVERT: H 299 ILE cc_start: 0.8570 (mt) cc_final: 0.8280 (pt) REVERT: H 302 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6981 (mm-30) REVERT: I 6 ILE cc_start: 0.9017 (mt) cc_final: 0.8492 (tp) REVERT: I 43 THR cc_start: 0.9577 (p) cc_final: 0.9064 (t) REVERT: I 54 TRP cc_start: 0.9147 (m-10) cc_final: 0.8916 (m-10) outliers start: 2 outliers final: 1 residues processed: 371 average time/residue: 0.1328 time to fit residues: 79.8674 Evaluate side-chains 263 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 211 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 126 optimal weight: 0.0370 chunk 56 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN C 227 HIS C 348 ASN D 96 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN E 348 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN G 281 ASN H 159 HIS J 14 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118945 restraints weight = 39805.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119422 restraints weight = 28731.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120007 restraints weight = 25316.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120860 restraints weight = 21175.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121064 restraints weight = 17257.142| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23187 Z= 0.221 Angle : 0.597 9.267 32030 Z= 0.318 Chirality : 0.041 0.232 3853 Planarity : 0.004 0.056 3906 Dihedral : 15.149 120.114 4592 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.06 % Allowed : 1.61 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.35 (0.15), residues: 2930 helix: 1.56 (0.18), residues: 929 sheet: 0.17 (0.23), residues: 514 loop : -1.63 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 191 TYR 0.023 0.002 TYR H 344 PHE 0.017 0.002 PHE D 166 TRP 0.033 0.002 TRP A 228 HIS 0.009 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00499 (23187) covalent geometry : angle 0.59672 (32030) hydrogen bonds : bond 0.03786 ( 962) hydrogen bonds : angle 4.86011 ( 2835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9522 (m-40) cc_final: 0.9234 (m110) REVERT: B 132 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7891 (tm-30) REVERT: B 288 GLU cc_start: 0.7265 (tt0) cc_final: 0.6850 (tt0) REVERT: C 216 GLU cc_start: 0.8568 (pp20) cc_final: 0.8286 (pp20) REVERT: C 238 ILE cc_start: 0.9267 (mm) cc_final: 0.8959 (tt) REVERT: C 316 GLN cc_start: 0.8859 (mm110) cc_final: 0.8551 (mm-40) REVERT: C 348 ASN cc_start: 0.8885 (t160) cc_final: 0.8604 (t0) REVERT: D 72 ILE cc_start: 0.9481 (mt) cc_final: 0.9273 (mm) REVERT: D 91 GLN cc_start: 0.8134 (mm110) cc_final: 0.7630 (mm110) REVERT: D 206 LYS cc_start: 0.8741 (mppt) cc_final: 0.8312 (mttt) REVERT: D 242 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8428 (tp40) REVERT: D 321 LEU cc_start: 0.8441 (mt) cc_final: 0.8012 (mp) REVERT: E 62 THR cc_start: 0.8834 (p) cc_final: 0.8478 (t) REVERT: E 124 THR cc_start: 0.9493 (m) cc_final: 0.9213 (p) REVERT: E 354 VAL cc_start: 0.9205 (t) cc_final: 0.8964 (p) REVERT: F 189 VAL cc_start: 0.9527 (t) cc_final: 0.9228 (m) REVERT: F 204 ASP cc_start: 0.7329 (p0) cc_final: 0.7070 (p0) REVERT: F 261 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8815 (mtmt) REVERT: F 277 GLN cc_start: 0.9065 (pm20) cc_final: 0.8730 (pm20) REVERT: G 94 ASN cc_start: 0.8453 (p0) cc_final: 0.8161 (p0) REVERT: G 106 ASP cc_start: 0.7652 (p0) cc_final: 0.7211 (p0) REVERT: G 109 THR cc_start: 0.8951 (m) cc_final: 0.8465 (p) REVERT: H 269 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7392 (mtm-85) REVERT: H 322 ASP cc_start: 0.7912 (t0) cc_final: 0.7682 (t70) REVERT: H 333 ARG cc_start: 0.8679 (mpp80) cc_final: 0.8330 (mpp80) REVERT: I 11 GLN cc_start: 0.8348 (tp40) cc_final: 0.7978 (tp-100) REVERT: I 43 THR cc_start: 0.9622 (p) cc_final: 0.9172 (t) REVERT: I 65 ILE cc_start: 0.9524 (mt) cc_final: 0.9313 (mm) REVERT: J 11 GLN cc_start: 0.8314 (tt0) cc_final: 0.7929 (tp40) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.1312 time to fit residues: 71.2088 Evaluate side-chains 254 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 6.9990 chunk 39 optimal weight: 50.0000 chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 40 optimal weight: 50.0000 chunk 293 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS B 305 HIS C 227 HIS C 281 ASN C 348 ASN D 129 ASN D 348 ASN E 348 ASN F 91 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN G 281 ASN G 348 ASN J 14 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118269 restraints weight = 39714.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120254 restraints weight = 26407.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121672 restraints weight = 19346.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122583 restraints weight = 15355.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123116 restraints weight = 12958.925| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23187 Z= 0.140 Angle : 0.521 8.547 32030 Z= 0.278 Chirality : 0.039 0.232 3853 Planarity : 0.004 0.047 3906 Dihedral : 15.012 118.059 4592 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.06 % Allowed : 1.26 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.16 (0.15), residues: 2930 helix: 1.75 (0.18), residues: 934 sheet: 0.37 (0.23), residues: 498 loop : -1.57 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 169 TYR 0.016 0.001 TYR G 290 PHE 0.016 0.001 PHE E 245 TRP 0.052 0.002 TRP B 316 HIS 0.008 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00314 (23187) covalent geometry : angle 0.52110 (32030) hydrogen bonds : bond 0.03156 ( 962) hydrogen bonds : angle 4.52792 ( 2835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.9524 (m-40) cc_final: 0.9244 (m110) REVERT: B 132 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7905 (tm-30) REVERT: B 288 GLU cc_start: 0.7243 (tt0) cc_final: 0.6828 (tt0) REVERT: C 211 LEU cc_start: 0.9108 (mm) cc_final: 0.8659 (mt) REVERT: C 216 GLU cc_start: 0.8515 (pp20) cc_final: 0.8275 (pp20) REVERT: C 238 ILE cc_start: 0.9225 (mm) cc_final: 0.8867 (tt) REVERT: C 348 ASN cc_start: 0.8738 (t160) cc_final: 0.8406 (t0) REVERT: D 74 ASN cc_start: 0.9002 (p0) cc_final: 0.8710 (p0) REVERT: D 91 GLN cc_start: 0.7932 (mm110) cc_final: 0.7396 (mm110) REVERT: D 143 THR cc_start: 0.8863 (p) cc_final: 0.8656 (t) REVERT: D 206 LYS cc_start: 0.8646 (mppt) cc_final: 0.8240 (mttt) REVERT: D 321 LEU cc_start: 0.8169 (mt) cc_final: 0.7745 (mp) REVERT: E 62 THR cc_start: 0.8814 (p) cc_final: 0.8476 (t) REVERT: E 124 THR cc_start: 0.9502 (m) cc_final: 0.9184 (p) REVERT: E 354 VAL cc_start: 0.9178 (t) cc_final: 0.8921 (p) REVERT: F 189 VAL cc_start: 0.9504 (t) cc_final: 0.9208 (m) REVERT: F 277 GLN cc_start: 0.9009 (pm20) cc_final: 0.8597 (pm20) REVERT: G 94 ASN cc_start: 0.8436 (p0) cc_final: 0.8126 (p0) REVERT: G 106 ASP cc_start: 0.7512 (p0) cc_final: 0.7049 (p0) REVERT: G 109 THR cc_start: 0.8906 (m) cc_final: 0.8434 (p) REVERT: G 277 GLN cc_start: 0.9058 (pm20) cc_final: 0.8638 (pm20) REVERT: H 269 ARG cc_start: 0.7778 (mmt90) cc_final: 0.7403 (mtm-85) REVERT: H 290 TYR cc_start: 0.8025 (p90) cc_final: 0.7468 (p90) REVERT: H 333 ARG cc_start: 0.8604 (mpp80) cc_final: 0.8400 (mpp80) REVERT: I 11 GLN cc_start: 0.8254 (tp40) cc_final: 0.7889 (tp-100) REVERT: I 43 THR cc_start: 0.9572 (p) cc_final: 0.9115 (t) REVERT: I 63 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7568 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.1227 time to fit residues: 71.0671 Evaluate side-chains 246 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 163 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 258 optimal weight: 0.4980 chunk 287 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 HIS C 348 ASN D 94 ASN D 348 ASN E 348 ASN F 91 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN G 281 ASN J 14 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120693 restraints weight = 39201.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122643 restraints weight = 25813.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123980 restraints weight = 18889.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124970 restraints weight = 14952.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125366 restraints weight = 12641.451| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23187 Z= 0.139 Angle : 0.529 12.461 32030 Z= 0.280 Chirality : 0.039 0.238 3853 Planarity : 0.004 0.044 3906 Dihedral : 14.953 117.719 4592 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.06 % Allowed : 0.80 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.08 (0.15), residues: 2930 helix: 1.79 (0.18), residues: 934 sheet: 0.51 (0.24), residues: 478 loop : -1.51 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 315 TYR 0.022 0.002 TYR D 344 PHE 0.012 0.001 PHE H 166 TRP 0.077 0.002 TRP B 316 HIS 0.012 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00312 (23187) covalent geometry : angle 0.52907 (32030) hydrogen bonds : bond 0.03165 ( 962) hydrogen bonds : angle 4.50882 ( 2835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.8546 (tpp80) cc_final: 0.7842 (ttp-170) REVERT: A 237 ASN cc_start: 0.9526 (m-40) cc_final: 0.9226 (m110) REVERT: B 132 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7957 (tm-30) REVERT: B 288 GLU cc_start: 0.7313 (tt0) cc_final: 0.6844 (tt0) REVERT: C 211 LEU cc_start: 0.8914 (mm) cc_final: 0.8637 (mt) REVERT: C 238 ILE cc_start: 0.9221 (mm) cc_final: 0.8910 (tt) REVERT: C 348 ASN cc_start: 0.8718 (t160) cc_final: 0.8400 (t0) REVERT: D 74 ASN cc_start: 0.9026 (p0) cc_final: 0.8671 (p0) REVERT: D 91 GLN cc_start: 0.7964 (mm110) cc_final: 0.7594 (mm110) REVERT: D 206 LYS cc_start: 0.8726 (mppt) cc_final: 0.8320 (mttt) REVERT: E 62 THR cc_start: 0.8816 (p) cc_final: 0.8464 (t) REVERT: E 124 THR cc_start: 0.9533 (m) cc_final: 0.9206 (p) REVERT: E 354 VAL cc_start: 0.9171 (t) cc_final: 0.8943 (p) REVERT: F 189 VAL cc_start: 0.9507 (t) cc_final: 0.9249 (m) REVERT: F 277 GLN cc_start: 0.9008 (pm20) cc_final: 0.8588 (pm20) REVERT: G 94 ASN cc_start: 0.8447 (p0) cc_final: 0.8125 (p0) REVERT: G 105 SER cc_start: 0.8019 (t) cc_final: 0.7777 (p) REVERT: G 106 ASP cc_start: 0.7646 (p0) cc_final: 0.7321 (p0) REVERT: G 277 GLN cc_start: 0.9119 (pm20) cc_final: 0.8630 (pm20) REVERT: H 49 TRP cc_start: 0.7899 (t60) cc_final: 0.7650 (t60) REVERT: H 87 ASP cc_start: 0.8217 (m-30) cc_final: 0.8002 (m-30) REVERT: H 243 GLU cc_start: 0.6923 (pt0) cc_final: 0.6566 (pt0) REVERT: H 269 ARG cc_start: 0.7854 (mmt90) cc_final: 0.7452 (mtm-85) REVERT: H 290 TYR cc_start: 0.8107 (p90) cc_final: 0.7532 (p90) REVERT: H 302 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6982 (mm-30) REVERT: I 11 GLN cc_start: 0.8281 (tp40) cc_final: 0.7920 (tp-100) REVERT: I 26 SER cc_start: 0.9151 (p) cc_final: 0.8867 (p) REVERT: I 43 THR cc_start: 0.9608 (p) cc_final: 0.9157 (t) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.1230 time to fit residues: 68.7792 Evaluate side-chains 237 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 90 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 256 optimal weight: 0.2980 chunk 205 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 278 optimal weight: 40.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN C 348 ASN D 348 ASN E 348 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 348 ASN H 159 HIS J 14 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121704 restraints weight = 39472.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123786 restraints weight = 25936.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125170 restraints weight = 18824.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126012 restraints weight = 14860.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126668 restraints weight = 12619.077| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23187 Z= 0.119 Angle : 0.508 11.576 32030 Z= 0.269 Chirality : 0.038 0.241 3853 Planarity : 0.004 0.072 3906 Dihedral : 14.873 117.355 4592 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.11 % Allowed : 0.86 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.02 (0.15), residues: 2930 helix: 1.91 (0.18), residues: 926 sheet: 0.55 (0.24), residues: 486 loop : -1.47 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 169 TYR 0.021 0.001 TYR C 324 PHE 0.020 0.001 PHE G 245 TRP 0.079 0.002 TRP B 316 HIS 0.010 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00266 (23187) covalent geometry : angle 0.50799 (32030) hydrogen bonds : bond 0.02940 ( 962) hydrogen bonds : angle 4.35736 ( 2835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.8509 (tpp80) cc_final: 0.7878 (ttp-170) REVERT: A 237 ASN cc_start: 0.9519 (m-40) cc_final: 0.9236 (m110) REVERT: B 132 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7928 (tm-30) REVERT: B 288 GLU cc_start: 0.7252 (tt0) cc_final: 0.6854 (tt0) REVERT: C 211 LEU cc_start: 0.8939 (mm) cc_final: 0.8601 (tp) REVERT: C 238 ILE cc_start: 0.9213 (mm) cc_final: 0.8887 (tt) REVERT: C 348 ASN cc_start: 0.8700 (t160) cc_final: 0.8241 (t0) REVERT: D 74 ASN cc_start: 0.9011 (p0) cc_final: 0.8748 (p0) REVERT: D 91 GLN cc_start: 0.7961 (mm110) cc_final: 0.7560 (mm110) REVERT: E 62 THR cc_start: 0.8801 (p) cc_final: 0.8483 (t) REVERT: E 124 THR cc_start: 0.9504 (m) cc_final: 0.9188 (p) REVERT: E 354 VAL cc_start: 0.9144 (t) cc_final: 0.8938 (p) REVERT: F 109 THR cc_start: 0.9275 (m) cc_final: 0.8704 (p) REVERT: F 189 VAL cc_start: 0.9508 (t) cc_final: 0.9239 (m) REVERT: F 277 GLN cc_start: 0.8972 (pm20) cc_final: 0.8519 (pm20) REVERT: F 332 LEU cc_start: 0.9130 (mm) cc_final: 0.8776 (mt) REVERT: G 94 ASN cc_start: 0.8410 (p0) cc_final: 0.8053 (p0) REVERT: G 106 ASP cc_start: 0.7495 (p0) cc_final: 0.6914 (p0) REVERT: G 270 ASP cc_start: 0.7741 (t0) cc_final: 0.7513 (t0) REVERT: G 277 GLN cc_start: 0.9080 (pm20) cc_final: 0.8607 (pm20) REVERT: H 49 TRP cc_start: 0.7808 (t60) cc_final: 0.7605 (t60) REVERT: H 184 ILE cc_start: 0.8960 (mm) cc_final: 0.8591 (mt) REVERT: H 243 GLU cc_start: 0.6884 (pt0) cc_final: 0.6421 (pt0) REVERT: H 269 ARG cc_start: 0.7797 (mmt90) cc_final: 0.7493 (mtm-85) REVERT: H 290 TYR cc_start: 0.8056 (p90) cc_final: 0.7443 (p90) REVERT: H 304 TYR cc_start: 0.8275 (m-80) cc_final: 0.8050 (m-10) REVERT: H 322 ASP cc_start: 0.7985 (t70) cc_final: 0.7750 (t0) REVERT: I 11 GLN cc_start: 0.8311 (tp40) cc_final: 0.7966 (tp-100) REVERT: I 26 SER cc_start: 0.9169 (p) cc_final: 0.8873 (p) REVERT: I 43 THR cc_start: 0.9578 (p) cc_final: 0.9125 (t) outliers start: 2 outliers final: 0 residues processed: 330 average time/residue: 0.1244 time to fit residues: 68.5733 Evaluate side-chains 231 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 283 optimal weight: 50.0000 chunk 244 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 220 optimal weight: 0.0370 chunk 30 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 31 optimal weight: 40.0000 chunk 7 optimal weight: 30.0000 chunk 301 optimal weight: 20.0000 chunk 277 optimal weight: 0.0040 overall best weight: 1.0272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN C 281 ASN C 316 GLN C 348 ASN D 348 ASN E 348 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN G 160 ASN ** G 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN J 14 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126098 restraints weight = 39569.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128007 restraints weight = 26562.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129302 restraints weight = 19543.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130285 restraints weight = 15513.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130781 restraints weight = 13076.213| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23187 Z= 0.098 Angle : 0.495 11.394 32030 Z= 0.258 Chirality : 0.038 0.232 3853 Planarity : 0.004 0.084 3906 Dihedral : 14.791 117.036 4592 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.06 % Allowed : 0.69 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.17 (0.15), residues: 2930 helix: 2.03 (0.18), residues: 927 sheet: 0.68 (0.24), residues: 477 loop : -1.38 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 169 TYR 0.014 0.001 TYR G 290 PHE 0.011 0.001 PHE G 166 TRP 0.050 0.001 TRP C 193 HIS 0.008 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00215 (23187) covalent geometry : angle 0.49483 (32030) hydrogen bonds : bond 0.02708 ( 962) hydrogen bonds : angle 4.24183 ( 2835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.8434 (tpp80) cc_final: 0.7859 (ttp-170) REVERT: A 237 ASN cc_start: 0.9512 (m-40) cc_final: 0.9220 (m110) REVERT: B 17 ILE cc_start: 0.9055 (mt) cc_final: 0.8717 (pt) REVERT: B 99 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8582 (mm-30) REVERT: B 132 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7877 (tm-30) REVERT: B 288 GLU cc_start: 0.7275 (tt0) cc_final: 0.6853 (tt0) REVERT: C 238 ILE cc_start: 0.9215 (mm) cc_final: 0.8880 (tt) REVERT: C 334 ASP cc_start: 0.8725 (m-30) cc_final: 0.8450 (m-30) REVERT: C 348 ASN cc_start: 0.8705 (t160) cc_final: 0.8227 (t0) REVERT: D 91 GLN cc_start: 0.7953 (mm110) cc_final: 0.7576 (mm110) REVERT: D 206 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8485 (mmtm) REVERT: E 62 THR cc_start: 0.8803 (p) cc_final: 0.8445 (t) REVERT: E 124 THR cc_start: 0.9485 (m) cc_final: 0.9177 (p) REVERT: F 189 VAL cc_start: 0.9488 (t) cc_final: 0.9255 (m) REVERT: F 202 LEU cc_start: 0.8340 (tp) cc_final: 0.8023 (tt) REVERT: F 277 GLN cc_start: 0.8920 (pm20) cc_final: 0.8441 (pm20) REVERT: F 332 LEU cc_start: 0.9039 (mm) cc_final: 0.8701 (mt) REVERT: G 94 ASN cc_start: 0.8331 (p0) cc_final: 0.7974 (p0) REVERT: G 106 ASP cc_start: 0.7459 (p0) cc_final: 0.6869 (p0) REVERT: G 189 VAL cc_start: 0.9309 (t) cc_final: 0.9014 (m) REVERT: G 270 ASP cc_start: 0.7728 (t0) cc_final: 0.7484 (t0) REVERT: G 277 GLN cc_start: 0.9050 (pm20) cc_final: 0.8623 (pm20) REVERT: H 184 ILE cc_start: 0.8860 (mm) cc_final: 0.8481 (mt) REVERT: H 269 ARG cc_start: 0.7832 (mmt90) cc_final: 0.7514 (mtm-85) REVERT: H 290 TYR cc_start: 0.8019 (p90) cc_final: 0.7381 (p90) REVERT: H 302 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6850 (mm-30) REVERT: H 304 TYR cc_start: 0.8193 (m-80) cc_final: 0.7992 (m-10) REVERT: H 322 ASP cc_start: 0.8015 (t70) cc_final: 0.7663 (t0) REVERT: I 11 GLN cc_start: 0.8292 (tp40) cc_final: 0.7917 (tp-100) REVERT: I 26 SER cc_start: 0.9108 (p) cc_final: 0.8843 (p) REVERT: I 43 THR cc_start: 0.9538 (p) cc_final: 0.9082 (t) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.1247 time to fit residues: 68.9406 Evaluate side-chains 245 residues out of total 2409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 66 optimal weight: 0.7980 chunk 231 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 48 optimal weight: 0.0060 chunk 8 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 190 optimal weight: 0.0870 overall best weight: 0.7776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN C 348 ASN D 348 ASN E 348 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 348 ASN J 14 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.128452 restraints weight = 39423.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130033 restraints weight = 26671.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130245 restraints weight = 21293.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131340 restraints weight = 17511.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131803 restraints weight = 14337.209| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23187 Z= 0.094 Angle : 0.497 11.442 32030 Z= 0.257 Chirality : 0.038 0.227 3853 Planarity : 0.004 0.089 3906 Dihedral : 14.750 116.125 4592 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.11 % Allowed : 0.40 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.25 (0.16), residues: 2930 helix: 2.07 (0.18), residues: 929 sheet: 0.75 (0.24), residues: 479 loop : -1.33 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.014 0.001 TYR H 290 PHE 0.013 0.001 PHE C 245 TRP 0.039 0.001 TRP B 316 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00207 (23187) covalent geometry : angle 0.49661 (32030) hydrogen bonds : bond 0.02607 ( 962) hydrogen bonds : angle 4.15725 ( 2835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.11 seconds wall clock time: 55 minutes 21.01 seconds (3321.01 seconds total)