Starting phenix.real_space_refine on Thu Mar 5 14:11:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e2c_30954/03_2026/7e2c_30954_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2c_30954/03_2026/7e2c_30954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e2c_30954/03_2026/7e2c_30954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2c_30954/03_2026/7e2c_30954.map" model { file = "/net/cci-nas-00/data/ceres_data/7e2c_30954/03_2026/7e2c_30954_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2c_30954/03_2026/7e2c_30954_neut.cif" } resolution = 4.18 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= 0.001 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: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 14589 2.51 5 N 3997 2.21 5 O 4348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 23020 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1206 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "B" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1458 Classifications: {'peptide': 195} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 38} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 4, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "D" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1234 Classifications: {'peptide': 151} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1295 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "G" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1612 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1172 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 4258 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 660} Link IDs: {'PTRANS': 17, 'TRANS': 781} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 2381 Unresolved non-hydrogen angles: 3030 Unresolved non-hydrogen dihedrals: 1971 Unresolved non-hydrogen chiralities: 227 Planarities with less than four sites: {'GLN:plan1': 29, 'PHE:plan': 43, 'GLU:plan': 62, 'ASP:plan': 38, 'HIS:plan': 9, 'TYR:plan': 24, 'ARG:plan': 25, 'ASN:plan1': 43, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 1266 Chain: "J" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6265 Classifications: {'peptide': 873} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 37, 'TRANS': 835} Chain breaks: 5 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 936 Unresolved non-hydrogen angles: 1195 Unresolved non-hydrogen dihedrals: 774 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 10, 'ASN:plan1': 15, 'PHE:plan': 9, 'TYR:plan': 14, 'ASP:plan': 20, 'TRP:plan': 3, 'GLU:plan': 11, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 448 Chain: "K" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1568 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'ASN:plan1': 10, 'ARG:plan': 5, 'GLU:plan': 8, 'HIS:plan': 4, 'ASP:plan': 5, 'PHE:plan': 5, 'GLN:plan1': 6, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 213 Time building chain proxies: 5.56, per 1000 atoms: 0.24 Number of scatterers: 23020 At special positions: 0 Unit cell: (193.107, 258.567, 146.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 4348 8.00 N 3997 7.00 C 14589 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: 1.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6340 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 35 sheets defined 30.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.959A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 121 removed outlier: 3.930A pdb=" N CYS A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.868A pdb=" N TYR B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 101 through 110 removed outlier: 3.658A pdb=" N HIS B 106 " --> pdb=" O HIS B 102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 4.046A pdb=" N ARG B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.826A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.991A pdb=" N MET B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 211' Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 230 removed outlier: 4.017A pdb=" N GLY B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 removed outlier: 4.846A pdb=" N GLY C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 45 removed outlier: 3.601A pdb=" N PHE C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 75 removed outlier: 3.824A pdb=" N ASN C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 97 removed outlier: 3.895A pdb=" N GLU C 88 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.594A pdb=" N CYS C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 removed outlier: 4.106A pdb=" N LYS D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 109 Processing helix chain 'D' and resid 142 through 154 removed outlier: 3.726A pdb=" N ILE D 146 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 47 removed outlier: 3.803A pdb=" N TYR E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 190 removed outlier: 3.652A pdb=" N ALA E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.766A pdb=" N LYS E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 18 removed outlier: 3.903A pdb=" N GLU F 15 " --> pdb=" O LYS F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 45 removed outlier: 4.054A pdb=" N PHE F 30 " --> pdb=" O ASN F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.953A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE F 68 " --> pdb=" O GLY F 64 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 99 removed outlier: 4.451A pdb=" N LYS F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.817A pdb=" N MET F 135 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS F 136 " --> pdb=" O ASP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 154 removed outlier: 3.689A pdb=" N LYS F 149 " --> pdb=" O CYS F 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 77 Processing helix chain 'G' and resid 79 through 107 removed outlier: 3.747A pdb=" N PHE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY G 91 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE G 96 " --> pdb=" O HIS G 92 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 187 removed outlier: 3.578A pdb=" N HIS G 184 " --> pdb=" O LEU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 242 removed outlier: 3.782A pdb=" N CYS G 234 " --> pdb=" O GLU G 230 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY G 235 " --> pdb=" O TYR G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 279 removed outlier: 3.536A pdb=" N LEU G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 4.410A pdb=" N TRP H 53 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 146 removed outlier: 3.525A pdb=" N TYR H 134 " --> pdb=" O MET H 130 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU H 139 " --> pdb=" O GLN H 135 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 169 removed outlier: 4.006A pdb=" N ARG H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.666A pdb=" N SER I 259 " --> pdb=" O SER I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 289 removed outlier: 3.896A pdb=" N PHE I 282 " --> pdb=" O HIS I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 314 Processing helix chain 'I' and resid 322 through 333 Processing helix chain 'I' and resid 334 through 337 Processing helix chain 'I' and resid 348 through 367 Processing helix chain 'I' and resid 399 through 409 Processing helix chain 'I' and resid 409 through 417 removed outlier: 3.938A pdb=" N SER I 415 " --> pdb=" O LYS I 411 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU I 416 " --> pdb=" O GLU I 412 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE I 417 " --> pdb=" O ILE I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 421 removed outlier: 3.803A pdb=" N GLU I 421 " --> pdb=" O ASN I 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 418 through 421' Processing helix chain 'I' and resid 456 through 460 removed outlier: 3.632A pdb=" N TYR I 459 " --> pdb=" O TYR I 456 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR I 460 " --> pdb=" O GLU I 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 456 through 460' Processing helix chain 'I' and resid 467 through 472 Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.516A pdb=" N HIS I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 526 removed outlier: 4.414A pdb=" N LYS I 523 " --> pdb=" O GLU I 519 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS I 524 " --> pdb=" O ILE I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 862 through 866 Processing helix chain 'I' and resid 867 through 869 No H-bonds generated for 'chain 'I' and resid 867 through 869' Processing helix chain 'I' and resid 886 through 888 No H-bonds generated for 'chain 'I' and resid 886 through 888' Processing helix chain 'I' and resid 889 through 894 Processing helix chain 'I' and resid 896 through 900 removed outlier: 3.635A pdb=" N LYS I 899 " --> pdb=" O GLU I 896 " (cutoff:3.500A) Processing helix chain 'I' and resid 921 through 924 removed outlier: 4.056A pdb=" N ASN I 924 " --> pdb=" O ILE I 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 921 through 924' Processing helix chain 'I' and resid 925 through 930 removed outlier: 4.215A pdb=" N LYS I 929 " --> pdb=" O LYS I 925 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE I 930 " --> pdb=" O THR I 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 925 through 930' Processing helix chain 'I' and resid 933 through 938 Processing helix chain 'I' and resid 939 through 947 Processing helix chain 'J' and resid 267 through 286 Processing helix chain 'J' and resid 310 through 328 Processing helix chain 'J' and resid 381 through 395 removed outlier: 3.816A pdb=" N MET J 385 " --> pdb=" O SER J 381 " (cutoff:3.500A) Proline residue: J 388 - end of helix Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 426 through 441 Proline residue: J 436 - end of helix Processing helix chain 'J' and resid 459 through 475 removed outlier: 4.402A pdb=" N LEU J 465 " --> pdb=" O SER J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 478 No H-bonds generated for 'chain 'J' and resid 476 through 478' Processing helix chain 'J' and resid 506 through 524 removed outlier: 3.612A pdb=" N GLN J 510 " --> pdb=" O GLN J 506 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR J 521 " --> pdb=" O MET J 517 " (cutoff:3.500A) Processing helix chain 'J' and resid 526 through 544 removed outlier: 3.751A pdb=" N GLN J 530 " --> pdb=" O TYR J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 553 through 563 Processing helix chain 'J' and resid 584 through 603 Processing helix chain 'J' and resid 604 through 619 Processing helix chain 'J' and resid 636 through 641 Processing helix chain 'J' and resid 897 through 905 Proline residue: J 903 - end of helix Processing helix chain 'J' and resid 920 through 924 removed outlier: 3.631A pdb=" N LEU J 924 " --> pdb=" O LEU J 921 " (cutoff:3.500A) Processing helix chain 'J' and resid 954 through 958 removed outlier: 4.271A pdb=" N PHE J 957 " --> pdb=" O ALA J 954 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1026 Processing helix chain 'J' and resid 1112 through 1129 removed outlier: 3.683A pdb=" N ARG J1118 " --> pdb=" O THR J1114 " (cutoff:3.500A) Processing helix chain 'J' and resid 1158 through 1163 removed outlier: 3.756A pdb=" N TYR J1162 " --> pdb=" O HIS J1158 " (cutoff:3.500A) Processing helix chain 'J' and resid 1197 through 1201 removed outlier: 3.558A pdb=" N CYS J1200 " --> pdb=" O THR J1197 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG J1201 " --> pdb=" O SER J1198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1197 through 1201' Processing helix chain 'K' and resid 237 through 249 removed outlier: 4.939A pdb=" N LEU K 243 " --> pdb=" O ALA K 239 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR K 244 " --> pdb=" O SER K 240 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE K 247 " --> pdb=" O LEU K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 500 removed outlier: 3.716A pdb=" N LEU K 489 " --> pdb=" O ASN K 485 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA K 497 " --> pdb=" O TYR K 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY K 499 " --> pdb=" O LYS K 495 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE K 500 " --> pdb=" O ILE K 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 4.563A pdb=" N ILE A 86 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 77 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA3, first strand: chain 'B' and resid 177 through 179 removed outlier: 3.721A pdb=" N THR B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.571A pdb=" N SER B 259 " --> pdb=" O CYS B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.678A pdb=" N LEU C 117 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 176 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 9 removed outlier: 3.954A pdb=" N SER D 5 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG D 68 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU E 4 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN E 20 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE E 6 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN E 18 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 8 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 24 through 25 Processing sheet with id=AA8, first strand: chain 'F' and resid 161 through 165 removed outlier: 6.986A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 209 through 213 Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 20 removed outlier: 3.528A pdb=" N ILE H 8 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET H 113 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR H 101 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP H 93 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA H 102 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS H 91 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE H 104 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU H 89 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 563 through 565 removed outlier: 3.805A pdb=" N MET I 580 " --> pdb=" O SER I 621 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU I 582 " --> pdb=" O GLU I 619 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 674 through 677 Processing sheet with id=AB4, first strand: chain 'I' and resid 742 through 745 Processing sheet with id=AB5, first strand: chain 'I' and resid 769 through 772 removed outlier: 3.714A pdb=" N ILE I 781 " --> pdb=" O LYS I 778 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 769 through 772 removed outlier: 4.012A pdb=" N PHE I 782 " --> pdb=" O ILE I 841 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 819 through 820 removed outlier: 4.943A pdb=" N LEU I 799 " --> pdb=" O ASN I 860 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN I 860 " --> pdb=" O LEU I 799 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER I 801 " --> pdb=" O ARG I 858 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN I 854 " --> pdb=" O SER I 805 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 983 through 984 removed outlier: 8.266A pdb=" N GLU I 983 " --> pdb=" O VAL I1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 987 through 992 Processing sheet with id=AC1, first strand: chain 'J' and resid 753 through 757 removed outlier: 3.659A pdb=" N SER J 804 " --> pdb=" O ILE J 754 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU J 756 " --> pdb=" O LYS J 802 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS J 802 " --> pdb=" O GLU J 756 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 860 through 861 removed outlier: 3.570A pdb=" N ASN J 861 " --> pdb=" O THR J 990 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'J' and resid 967 through 970 Processing sheet with id=AC4, first strand: chain 'J' and resid 995 through 996 Processing sheet with id=AC5, first strand: chain 'J' and resid 995 through 996 Processing sheet with id=AC6, first strand: chain 'J' and resid 1055 through 1057 removed outlier: 3.634A pdb=" N ASN J1134 " --> pdb=" O ASN J1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 1172 through 1177 Processing sheet with id=AC8, first strand: chain 'J' and resid 1181 through 1182 removed outlier: 3.502A pdb=" N VAL J1182 " --> pdb=" O SER J1287 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 1208 through 1209 Processing sheet with id=AD1, first strand: chain 'J' and resid 1231 through 1232 Processing sheet with id=AD2, first strand: chain 'K' and resid 217 through 221 Processing sheet with id=AD3, first strand: chain 'K' and resid 283 through 284 Processing sheet with id=AD4, first strand: chain 'K' and resid 267 through 268 removed outlier: 4.317A pdb=" N LYS K 306 " --> pdb=" O LEU K 268 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 310 through 311 Processing sheet with id=AD6, first strand: chain 'K' and resid 411 through 414 Processing sheet with id=AD7, first strand: chain 'K' and resid 420 through 421 removed outlier: 5.909A pdb=" N LYS K 420 " --> pdb=" O VAL K 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'K' and resid 444 through 446 767 hydrogen bonds defined for protein. 2157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6858 1.34 - 1.46: 4929 1.46 - 1.58: 11447 1.58 - 1.70: 1 1.70 - 1.83: 134 Bond restraints: 23369 Sorted by residual: bond pdb=" N PHE G 215 " pdb=" CA PHE G 215 " ideal model delta sigma weight residual 1.463 1.421 0.042 9.30e-03 1.16e+04 2.04e+01 bond pdb=" N PHE H 29 " pdb=" CA PHE H 29 " ideal model delta sigma weight residual 1.457 1.488 -0.032 9.10e-03 1.21e+04 1.23e+01 bond pdb=" N ILE H 40 " pdb=" CA ILE H 40 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.73e+00 bond pdb=" C PHE J 485 " pdb=" N PRO J 486 " ideal model delta sigma weight residual 1.330 1.366 -0.036 1.23e-02 6.61e+03 8.61e+00 bond pdb=" N VAL J 955 " pdb=" CA VAL J 955 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.17e+00 ... (remaining 23364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 31222 4.58 - 9.17: 532 9.17 - 13.75: 54 13.75 - 18.33: 11 18.33 - 22.92: 4 Bond angle restraints: 31823 Sorted by residual: angle pdb=" N PRO I 346 " pdb=" CA PRO I 346 " pdb=" CB PRO I 346 " ideal model delta sigma weight residual 102.28 110.18 -7.90 7.50e-01 1.78e+00 1.11e+02 angle pdb=" N PRO I 976 " pdb=" CA PRO I 976 " pdb=" CB PRO I 976 " ideal model delta sigma weight residual 103.25 112.79 -9.54 1.05e+00 9.07e-01 8.26e+01 angle pdb=" N PRO I1076 " pdb=" CA PRO I1076 " pdb=" CB PRO I1076 " ideal model delta sigma weight residual 103.25 112.05 -8.80 1.05e+00 9.07e-01 7.02e+01 angle pdb=" N PRO H 26 " pdb=" CA PRO H 26 " pdb=" CB PRO H 26 " ideal model delta sigma weight residual 103.25 111.90 -8.65 1.05e+00 9.07e-01 6.79e+01 angle pdb=" N PRO K 325 " pdb=" CA PRO K 325 " pdb=" CB PRO K 325 " ideal model delta sigma weight residual 103.25 111.80 -8.55 1.05e+00 9.07e-01 6.63e+01 ... (remaining 31818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 12415 17.00 - 34.00: 1319 34.00 - 51.00: 207 51.00 - 68.00: 53 68.00 - 85.00: 18 Dihedral angle restraints: 14012 sinusoidal: 4312 harmonic: 9700 Sorted by residual: dihedral pdb=" CA SER A 132 " pdb=" C SER A 132 " pdb=" N ILE A 133 " pdb=" CA ILE A 133 " ideal model delta harmonic sigma weight residual 180.00 150.08 29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ARG I1051 " pdb=" C ARG I1051 " pdb=" N CYS I1052 " pdb=" CA CYS I1052 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLU J 563 " pdb=" C GLU J 563 " pdb=" N LEU J 564 " pdb=" CA LEU J 564 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 14009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3370 0.120 - 0.240: 363 0.240 - 0.360: 48 0.360 - 0.480: 14 0.480 - 0.600: 4 Chirality restraints: 3799 Sorted by residual: chirality pdb=" CB VAL F 155 " pdb=" CA VAL F 155 " pdb=" CG1 VAL F 155 " pdb=" CG2 VAL F 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" CB ILE E 172 " pdb=" CA ILE E 172 " pdb=" CG1 ILE E 172 " pdb=" CG2 ILE E 172 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CB ILE E 70 " pdb=" CA ILE E 70 " pdb=" CG1 ILE E 70 " pdb=" CG2 ILE E 70 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.14e+00 ... (remaining 3796 not shown) Planarity restraints: 4159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 67 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO E 68 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 68 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 68 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 633 " -0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C LYS J 633 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS J 633 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU J 634 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 635 " 0.018 2.00e-02 2.50e+03 2.87e-02 1.64e+01 pdb=" CG TYR J 635 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR J 635 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR J 635 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 635 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR J 635 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR J 635 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR J 635 " 0.011 2.00e-02 2.50e+03 ... (remaining 4156 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 10 2.32 - 2.96: 10749 2.96 - 3.61: 34379 3.61 - 4.25: 47829 4.25 - 4.90: 77204 Nonbonded interactions: 170171 Sorted by model distance: nonbonded pdb=" CG2 ILE A 79 " pdb=" OE1 GLN A 81 " model vdw 1.675 3.460 nonbonded pdb=" CE LYS A 35 " pdb=" CB ASP I 377 " model vdw 1.831 3.840 nonbonded pdb=" O ASN I 379 " pdb=" O TYR I 380 " model vdw 2.021 3.040 nonbonded pdb=" NZ LYS A 35 " pdb=" CA ASP I 377 " model vdw 2.212 3.550 nonbonded pdb=" OH TYR H 4 " pdb=" OD1 ASN H 37 " model vdw 2.249 3.040 ... (remaining 170166 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 8 through 189) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 10.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.770 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 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 : 0.008 0.093 23369 Z= 0.422 Angle : 1.501 22.918 31823 Z= 0.837 Chirality : 0.083 0.600 3799 Planarity : 0.008 0.117 4159 Dihedral : 15.124 85.001 7672 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 1.08 % Allowed : 15.30 % Favored : 83.62 % Rotamer: Outliers : 0.94 % Allowed : 1.99 % Favored : 97.07 % Cbeta Deviations : 0.09 % 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: -5.41 (0.11), residues: 3235 helix: -3.32 (0.11), residues: 967 sheet: -2.88 (0.21), residues: 520 loop : -4.12 (0.11), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 555 TYR 0.052 0.004 TYR K 447 PHE 0.058 0.004 PHE I 784 TRP 0.048 0.004 TRP I1024 HIS 0.013 0.002 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00846 (23369) covalent geometry : angle 1.50135 (31823) hydrogen bonds : bond 0.21844 ( 761) hydrogen bonds : angle 9.24210 ( 2157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 418 time to evaluate : 0.921 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 8 VAL cc_start: 0.8931 (t) cc_final: 0.8506 (t) REVERT: A 88 ILE cc_start: 0.7376 (mm) cc_final: 0.6895 (mm) REVERT: A 93 LYS cc_start: 0.5155 (OUTLIER) cc_final: 0.4726 (tppp) REVERT: A 131 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8431 (tmtt) REVERT: B 151 MET cc_start: 0.7226 (pmm) cc_final: 0.6636 (pmm) REVERT: B 181 ARG cc_start: 0.7520 (mpt180) cc_final: 0.7305 (mtm-85) REVERT: C 59 MET cc_start: 0.7154 (ttt) cc_final: 0.6313 (ttm) REVERT: C 135 MET cc_start: 0.2034 (tpt) cc_final: 0.1646 (tpp) REVERT: C 154 MET cc_start: 0.6290 (mmp) cc_final: 0.6082 (mmt) REVERT: D 36 GLN cc_start: 0.6679 (mp-120) cc_final: 0.6393 (mm110) REVERT: E 21 PHE cc_start: 0.8175 (m-80) cc_final: 0.7825 (m-80) REVERT: E 174 ILE cc_start: 0.7503 (tt) cc_final: 0.7084 (mm) REVERT: F 27 THR cc_start: 0.7553 (p) cc_final: 0.7275 (t) REVERT: F 62 ASN cc_start: 0.8560 (t0) cc_final: 0.7842 (t0) REVERT: F 188 ILE cc_start: 0.7672 (mm) cc_final: 0.7011 (tt) REVERT: G 69 MET cc_start: 0.8643 (ttp) cc_final: 0.8415 (ttm) REVERT: G 212 VAL cc_start: 0.8213 (t) cc_final: 0.7964 (t) REVERT: G 230 GLU cc_start: 0.7797 (pm20) cc_final: 0.7594 (pm20) REVERT: G 236 ILE cc_start: 0.8786 (tp) cc_final: 0.8543 (tp) REVERT: G 238 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7864 (tttp) REVERT: H 16 TYR cc_start: 0.7627 (t80) cc_final: 0.7171 (t80) REVERT: H 17 GLU cc_start: 0.6428 (pm20) cc_final: 0.5766 (tt0) REVERT: J 787 ILE cc_start: 0.5917 (mp) cc_final: 0.5651 (mp) REVERT: J 902 LYS cc_start: 0.8196 (tptp) cc_final: 0.7925 (tppt) REVERT: J 1226 ARG cc_start: 0.7881 (mpp80) cc_final: 0.7519 (mtm180) REVERT: K 496 ILE cc_start: 0.9032 (mt) cc_final: 0.8825 (mm) outliers start: 18 outliers final: 9 residues processed: 434 average time/residue: 0.1704 time to fit residues: 115.0752 Evaluate side-chains 262 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 252 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN C 20 ASN C 53 ASN C 181 ASN D 142 ASN E 177 ASN G 164 ASN G 243 ASN G 253 HIS ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN J1174 GLN ** K 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.098780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.092395 restraints weight = 110630.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.092143 restraints weight = 138640.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.092418 restraints weight = 128578.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091981 restraints weight = 98593.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.092006 restraints weight = 101942.627| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 105 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 108 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 23369 Z= 0.230 Angle : 0.823 12.824 31823 Z= 0.443 Chirality : 0.050 0.231 3799 Planarity : 0.006 0.091 4159 Dihedral : 7.170 30.822 3449 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.03 % Favored : 85.69 % Rotamer: Outliers : 0.47 % Allowed : 10.29 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.13), residues: 3235 helix: -1.94 (0.14), residues: 1005 sheet: -2.58 (0.22), residues: 500 loop : -4.11 (0.12), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 139 TYR 0.025 0.002 TYR J 648 PHE 0.032 0.002 PHE A 109 TRP 0.021 0.003 TRP F 18 HIS 0.012 0.002 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00520 (23369) covalent geometry : angle 0.82255 (31823) hydrogen bonds : bond 0.05187 ( 761) hydrogen bonds : angle 6.43993 ( 2157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 317 time to evaluate : 0.967 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: B 151 MET cc_start: 0.6629 (pmm) cc_final: 0.5787 (pmm) REVERT: B 158 LYS cc_start: 0.6564 (ptpt) cc_final: 0.6227 (ptpt) REVERT: C 154 MET cc_start: 0.7059 (mmp) cc_final: 0.6770 (mmp) REVERT: E 191 MET cc_start: 0.7346 (mmm) cc_final: 0.6799 (mmm) REVERT: F 13 MET cc_start: 0.8018 (ppp) cc_final: 0.6657 (ppp) REVERT: F 62 ASN cc_start: 0.8256 (t0) cc_final: 0.7921 (t0) REVERT: H 42 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7572 (m-70) REVERT: J 536 LEU cc_start: 0.7945 (mp) cc_final: 0.7676 (mt) REVERT: J 745 ILE cc_start: 0.7102 (tt) cc_final: 0.6894 (tt) outliers start: 9 outliers final: 3 residues processed: 323 average time/residue: 0.1674 time to fit residues: 84.6445 Evaluate side-chains 223 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 282 optimal weight: 0.0870 chunk 171 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN D 14 ASN F 100 ASN G 92 HIS G 164 ASN G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 448 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.100759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.093989 restraints weight = 109808.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.093876 restraints weight = 135787.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.094227 restraints weight = 120386.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.094100 restraints weight = 87290.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.094217 restraints weight = 84092.045| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 108 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23369 Z= 0.148 Angle : 0.718 11.942 31823 Z= 0.382 Chirality : 0.048 0.238 3799 Planarity : 0.005 0.072 4159 Dihedral : 6.343 23.641 3449 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.36 % Favored : 87.42 % Rotamer: Outliers : 0.21 % Allowed : 5.64 % Favored : 94.15 % 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: -4.16 (0.13), residues: 3235 helix: -1.30 (0.15), residues: 1014 sheet: -2.28 (0.23), residues: 483 loop : -4.00 (0.12), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 555 TYR 0.018 0.002 TYR D 4 PHE 0.025 0.002 PHE B 184 TRP 0.022 0.002 TRP I1024 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00326 (23369) covalent geometry : angle 0.71829 (31823) hydrogen bonds : bond 0.04464 ( 761) hydrogen bonds : angle 5.89253 ( 2157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 342 time to evaluate : 0.944 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: B 158 LYS cc_start: 0.6507 (ptpt) cc_final: 0.6171 (ptpt) REVERT: B 168 ILE cc_start: 0.7624 (pt) cc_final: 0.7233 (mt) REVERT: D 4 TYR cc_start: 0.7589 (m-10) cc_final: 0.7353 (m-10) REVERT: E 191 MET cc_start: 0.7142 (mmm) cc_final: 0.6654 (mmm) REVERT: F 116 SER cc_start: 0.6027 (p) cc_final: 0.5658 (p) REVERT: J 536 LEU cc_start: 0.8108 (mp) cc_final: 0.7705 (tp) REVERT: J 1226 ARG cc_start: 0.6922 (mpp80) cc_final: 0.6459 (mtm180) outliers start: 4 outliers final: 0 residues processed: 344 average time/residue: 0.1552 time to fit residues: 85.4466 Evaluate side-chains 225 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 242 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 147 optimal weight: 0.0000 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 276 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 263 GLN D 14 ASN D 142 ASN G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 551 HIS J 628 GLN J1174 GLN J1205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.101072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.093871 restraints weight = 108952.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.093636 restraints weight = 130033.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.094135 restraints weight = 113384.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.093963 restraints weight = 85054.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.094037 restraints weight = 84133.190| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23369 Z= 0.142 Angle : 0.686 11.618 31823 Z= 0.364 Chirality : 0.047 0.186 3799 Planarity : 0.004 0.066 4159 Dihedral : 5.893 25.144 3449 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.86 % Favored : 86.92 % Rotamer: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -3.82 (0.14), residues: 3235 helix: -0.86 (0.16), residues: 1003 sheet: -2.09 (0.23), residues: 482 loop : -3.89 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.018 0.002 TYR H 103 PHE 0.022 0.002 PHE B 184 TRP 0.023 0.002 TRP I1024 HIS 0.004 0.001 HIS G 74 Details of bonding type rmsd covalent geometry : bond 0.00317 (23369) covalent geometry : angle 0.68627 (31823) hydrogen bonds : bond 0.04071 ( 761) hydrogen bonds : angle 5.53633 ( 2157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.934 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: A 90 PHE cc_start: 0.7835 (m-80) cc_final: 0.7616 (m-10) REVERT: B 151 MET cc_start: 0.6498 (pmm) cc_final: 0.5991 (pmm) REVERT: C 112 LYS cc_start: 0.4962 (mmtt) cc_final: 0.4626 (tptt) REVERT: C 135 MET cc_start: 0.4668 (mmm) cc_final: 0.4157 (tpp) REVERT: C 154 MET cc_start: 0.6882 (mmt) cc_final: 0.6598 (mmt) REVERT: D 4 TYR cc_start: 0.7653 (m-10) cc_final: 0.7261 (m-80) REVERT: D 106 ILE cc_start: 0.9134 (pt) cc_final: 0.8742 (tt) REVERT: D 132 MET cc_start: 0.3622 (pmm) cc_final: 0.3328 (pmm) REVERT: E 191 MET cc_start: 0.7147 (mmm) cc_final: 0.6656 (mmt) REVERT: F 13 MET cc_start: 0.7883 (ppp) cc_final: 0.6371 (mmt) REVERT: F 75 THR cc_start: 0.7745 (p) cc_final: 0.7382 (m) REVERT: F 116 SER cc_start: 0.6134 (p) cc_final: 0.5497 (t) REVERT: G 89 ASP cc_start: 0.7735 (p0) cc_final: 0.6794 (t0) REVERT: J 536 LEU cc_start: 0.8149 (mp) cc_final: 0.7737 (tp) REVERT: J 1217 ASP cc_start: 0.5567 (t70) cc_final: 0.5241 (t70) REVERT: J 1226 ARG cc_start: 0.6954 (mpp80) cc_final: 0.6597 (mtm180) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1534 time to fit residues: 83.3042 Evaluate side-chains 237 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 101 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 233 optimal weight: 0.0870 chunk 254 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 82 optimal weight: 0.0670 chunk 29 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.0298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 ASN D 142 ASN F 20 ASN G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.099891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092740 restraints weight = 108491.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092570 restraints weight = 136545.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.092994 restraints weight = 112776.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.092877 restraints weight = 86908.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092939 restraints weight = 82022.738| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23369 Z= 0.162 Angle : 0.709 11.838 31823 Z= 0.374 Chirality : 0.048 0.198 3799 Planarity : 0.004 0.067 4159 Dihedral : 5.844 22.466 3449 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.66 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -3.75 (0.14), residues: 3235 helix: -0.77 (0.16), residues: 1017 sheet: -2.16 (0.23), residues: 499 loop : -3.85 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 528 TYR 0.017 0.002 TYR J 491 PHE 0.020 0.002 PHE J 757 TRP 0.028 0.002 TRP I1024 HIS 0.005 0.001 HIS J 621 Details of bonding type rmsd covalent geometry : bond 0.00367 (23369) covalent geometry : angle 0.70910 (31823) hydrogen bonds : bond 0.04164 ( 761) hydrogen bonds : angle 5.51072 ( 2157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.2962 (tpp) cc_final: 0.2534 (mmm) REVERT: B 151 MET cc_start: 0.6574 (pmm) cc_final: 0.6317 (pmm) REVERT: C 59 MET cc_start: 0.6096 (ttt) cc_final: 0.5711 (ttm) REVERT: C 135 MET cc_start: 0.4682 (mmm) cc_final: 0.4360 (tpp) REVERT: C 154 MET cc_start: 0.7019 (mmt) cc_final: 0.6678 (mmt) REVERT: D 4 TYR cc_start: 0.7698 (m-10) cc_final: 0.7327 (m-80) REVERT: D 82 THR cc_start: 0.8144 (p) cc_final: 0.7903 (p) REVERT: D 132 MET cc_start: 0.3834 (pmm) cc_final: 0.3563 (pmm) REVERT: E 191 MET cc_start: 0.7337 (mmm) cc_final: 0.6756 (mmm) REVERT: F 75 THR cc_start: 0.7963 (p) cc_final: 0.7723 (m) REVERT: F 116 SER cc_start: 0.6353 (p) cc_final: 0.5834 (t) REVERT: G 68 GLU cc_start: 0.6839 (tp30) cc_final: 0.6235 (tp30) REVERT: G 89 ASP cc_start: 0.7904 (p0) cc_final: 0.6899 (t0) REVERT: G 204 GLU cc_start: 0.7526 (pt0) cc_final: 0.7314 (pt0) REVERT: J 536 LEU cc_start: 0.8061 (mp) cc_final: 0.7722 (tp) REVERT: J 1226 ARG cc_start: 0.6871 (mpp80) cc_final: 0.6499 (mtm180) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1457 time to fit residues: 75.5541 Evaluate side-chains 229 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 324 optimal weight: 0.5980 chunk 277 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 270 optimal weight: 0.0060 chunk 213 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 300 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 ASN G 92 HIS G 220 GLN G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.099739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092880 restraints weight = 109245.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.092798 restraints weight = 123044.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.093189 restraints weight = 108877.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.093160 restraints weight = 81759.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.093258 restraints weight = 85273.446| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23369 Z= 0.168 Angle : 0.702 13.882 31823 Z= 0.371 Chirality : 0.048 0.256 3799 Planarity : 0.004 0.069 4159 Dihedral : 5.827 24.475 3449 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.82 % Favored : 85.97 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -3.62 (0.14), residues: 3235 helix: -0.62 (0.16), residues: 1002 sheet: -2.17 (0.23), residues: 486 loop : -3.75 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J1202 TYR 0.018 0.002 TYR J 491 PHE 0.023 0.002 PHE I 784 TRP 0.030 0.002 TRP I1024 HIS 0.008 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00381 (23369) covalent geometry : angle 0.70172 (31823) hydrogen bonds : bond 0.04169 ( 761) hydrogen bonds : angle 5.46002 ( 2157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7356 (p0) cc_final: 0.6776 (m-30) REVERT: C 101 ILE cc_start: 0.6007 (pt) cc_final: 0.5740 (pt) REVERT: C 135 MET cc_start: 0.4610 (mmm) cc_final: 0.4186 (tpp) REVERT: D 4 TYR cc_start: 0.7736 (m-10) cc_final: 0.7327 (m-80) REVERT: D 82 THR cc_start: 0.8241 (p) cc_final: 0.8006 (p) REVERT: F 13 MET cc_start: 0.7988 (ppp) cc_final: 0.7587 (ppp) REVERT: F 17 ILE cc_start: 0.8425 (pt) cc_final: 0.8133 (pt) REVERT: F 116 SER cc_start: 0.6249 (p) cc_final: 0.6032 (p) REVERT: G 68 GLU cc_start: 0.6417 (tp30) cc_final: 0.6071 (tp30) REVERT: G 204 GLU cc_start: 0.7359 (pt0) cc_final: 0.7153 (pt0) REVERT: J 536 LEU cc_start: 0.8113 (mp) cc_final: 0.7755 (tp) REVERT: J 561 ILE cc_start: 0.9417 (tp) cc_final: 0.9136 (tt) REVERT: J 1226 ARG cc_start: 0.6782 (mpp80) cc_final: 0.6386 (mtm180) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1477 time to fit residues: 75.0207 Evaluate side-chains 231 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 173 optimal weight: 0.0970 chunk 325 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 275 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.099063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.092481 restraints weight = 109798.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.092211 restraints weight = 133911.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.092503 restraints weight = 122808.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.092461 restraints weight = 96031.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.092528 restraints weight = 91674.970| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23369 Z= 0.194 Angle : 0.743 13.107 31823 Z= 0.394 Chirality : 0.049 0.248 3799 Planarity : 0.004 0.061 4159 Dihedral : 5.961 25.415 3449 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.99 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -3.64 (0.14), residues: 3235 helix: -0.67 (0.16), residues: 999 sheet: -2.16 (0.23), residues: 480 loop : -3.74 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J1202 TYR 0.026 0.002 TYR H 103 PHE 0.022 0.002 PHE J 757 TRP 0.032 0.002 TRP I1024 HIS 0.009 0.001 HIS G 74 Details of bonding type rmsd covalent geometry : bond 0.00441 (23369) covalent geometry : angle 0.74349 (31823) hydrogen bonds : bond 0.04414 ( 761) hydrogen bonds : angle 5.56289 ( 2157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8131 (p) cc_final: 0.7912 (m) REVERT: B 151 MET cc_start: 0.6363 (pmm) cc_final: 0.6141 (pmm) REVERT: B 163 ASP cc_start: 0.7237 (p0) cc_final: 0.6638 (m-30) REVERT: C 101 ILE cc_start: 0.6091 (pt) cc_final: 0.5863 (pt) REVERT: C 135 MET cc_start: 0.4714 (mmm) cc_final: 0.4258 (tpp) REVERT: D 82 THR cc_start: 0.8328 (p) cc_final: 0.8118 (p) REVERT: F 13 MET cc_start: 0.7796 (ppp) cc_final: 0.6954 (ppp) REVERT: F 17 ILE cc_start: 0.8233 (pt) cc_final: 0.7826 (pt) REVERT: F 116 SER cc_start: 0.6158 (p) cc_final: 0.5925 (p) REVERT: F 162 TRP cc_start: 0.6443 (p90) cc_final: 0.6149 (p90) REVERT: G 68 GLU cc_start: 0.6520 (tp30) cc_final: 0.6196 (tp30) REVERT: G 89 ASP cc_start: 0.7964 (p0) cc_final: 0.6952 (t0) REVERT: H 44 SER cc_start: 0.8553 (m) cc_final: 0.8135 (m) REVERT: J 536 LEU cc_start: 0.7990 (mp) cc_final: 0.7708 (mt) REVERT: J 561 ILE cc_start: 0.9430 (tp) cc_final: 0.9209 (tt) REVERT: J 1226 ARG cc_start: 0.6733 (mpp80) cc_final: 0.6382 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1517 time to fit residues: 73.5439 Evaluate side-chains 222 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 201 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 276 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.100502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.093569 restraints weight = 108628.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.093407 restraints weight = 126423.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.093716 restraints weight = 117183.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.093520 restraints weight = 97056.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.093727 restraints weight = 90174.062| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 107 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 108 | |-----------------------------------------------------------------------------| r_final: 0.3733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23369 Z= 0.142 Angle : 0.694 13.110 31823 Z= 0.364 Chirality : 0.048 0.229 3799 Planarity : 0.004 0.062 4159 Dihedral : 5.665 24.479 3449 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.26 % Favored : 86.52 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -3.53 (0.14), residues: 3235 helix: -0.55 (0.16), residues: 1023 sheet: -2.05 (0.23), residues: 484 loop : -3.75 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J1202 TYR 0.019 0.002 TYR D 4 PHE 0.022 0.002 PHE I 784 TRP 0.029 0.002 TRP I1024 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00319 (23369) covalent geometry : angle 0.69356 (31823) hydrogen bonds : bond 0.03999 ( 761) hydrogen bonds : angle 5.32542 ( 2157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.2594 (tpp) cc_final: 0.2287 (mmt) REVERT: C 59 MET cc_start: 0.5990 (ttt) cc_final: 0.5645 (ttm) REVERT: C 135 MET cc_start: 0.4590 (mmm) cc_final: 0.3979 (tpp) REVERT: D 82 THR cc_start: 0.8217 (p) cc_final: 0.8003 (p) REVERT: F 13 MET cc_start: 0.7936 (ppp) cc_final: 0.7587 (ppp) REVERT: F 17 ILE cc_start: 0.8398 (pt) cc_final: 0.8047 (pt) REVERT: F 116 SER cc_start: 0.6277 (p) cc_final: 0.5928 (p) REVERT: F 162 TRP cc_start: 0.6398 (p90) cc_final: 0.6132 (p90) REVERT: G 89 ASP cc_start: 0.8026 (p0) cc_final: 0.6889 (t0) REVERT: J 470 LYS cc_start: 0.7333 (tmmt) cc_final: 0.7103 (ttpt) REVERT: J 561 ILE cc_start: 0.9404 (tp) cc_final: 0.9181 (tt) REVERT: J 1217 ASP cc_start: 0.5576 (t70) cc_final: 0.5149 (t70) REVERT: J 1226 ARG cc_start: 0.6661 (mpp80) cc_final: 0.6447 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1502 time to fit residues: 75.5236 Evaluate side-chains 230 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 162 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 chunk 239 optimal weight: 0.0970 chunk 287 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.100802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.094258 restraints weight = 109728.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.094080 restraints weight = 137620.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.094410 restraints weight = 118651.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.094416 restraints weight = 89899.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.094437 restraints weight = 87707.638| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 108 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 108 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23369 Z= 0.139 Angle : 0.695 12.818 31823 Z= 0.364 Chirality : 0.048 0.225 3799 Planarity : 0.004 0.064 4159 Dihedral : 5.521 23.649 3449 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.14 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -3.42 (0.14), residues: 3235 helix: -0.38 (0.17), residues: 1007 sheet: -2.05 (0.23), residues: 482 loop : -3.68 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 528 TYR 0.019 0.002 TYR B 185 PHE 0.027 0.002 PHE G 221 TRP 0.086 0.002 TRP J 584 HIS 0.007 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00311 (23369) covalent geometry : angle 0.69547 (31823) hydrogen bonds : bond 0.03944 ( 761) hydrogen bonds : angle 5.24917 ( 2157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7283 (p0) cc_final: 0.6735 (m-30) REVERT: C 112 LYS cc_start: 0.4794 (mptt) cc_final: 0.4542 (mptt) REVERT: C 132 MET cc_start: 0.6356 (mmm) cc_final: 0.5784 (mmt) REVERT: C 135 MET cc_start: 0.4814 (mmm) cc_final: 0.4396 (tpp) REVERT: D 82 THR cc_start: 0.8038 (p) cc_final: 0.7772 (p) REVERT: F 13 MET cc_start: 0.7774 (ppp) cc_final: 0.7095 (ppp) REVERT: F 17 ILE cc_start: 0.8665 (pt) cc_final: 0.8376 (pt) REVERT: F 116 SER cc_start: 0.6260 (p) cc_final: 0.5939 (p) REVERT: F 162 TRP cc_start: 0.6405 (p90) cc_final: 0.6150 (p90) REVERT: G 89 ASP cc_start: 0.8005 (p0) cc_final: 0.6905 (t0) REVERT: G 238 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7945 (tttp) REVERT: J 561 ILE cc_start: 0.9397 (tp) cc_final: 0.9151 (tt) REVERT: J 1217 ASP cc_start: 0.5627 (t70) cc_final: 0.5219 (t70) REVERT: J 1226 ARG cc_start: 0.6603 (mpp80) cc_final: 0.6372 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1458 time to fit residues: 73.2130 Evaluate side-chains 224 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 12 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 320 optimal weight: 0.4980 chunk 192 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 124 optimal weight: 0.0670 chunk 171 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.101283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.094892 restraints weight = 109431.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.094527 restraints weight = 150142.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.094935 restraints weight = 131713.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.095010 restraints weight = 101592.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.095028 restraints weight = 99675.342| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23369 Z= 0.136 Angle : 0.691 12.874 31823 Z= 0.361 Chirality : 0.048 0.228 3799 Planarity : 0.004 0.059 4159 Dihedral : 5.402 24.249 3449 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.89 % Favored : 86.89 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -3.30 (0.14), residues: 3235 helix: -0.27 (0.17), residues: 1005 sheet: -1.92 (0.23), residues: 472 loop : -3.63 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 528 TYR 0.032 0.002 TYR H 103 PHE 0.024 0.002 PHE I 784 TRP 0.030 0.002 TRP I1024 HIS 0.006 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00304 (23369) covalent geometry : angle 0.69083 (31823) hydrogen bonds : bond 0.03841 ( 761) hydrogen bonds : angle 5.19607 ( 2157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6470 Ramachandran restraints generated. 3235 Oldfield, 0 Emsley, 3235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.2630 (tpp) cc_final: 0.2335 (mmt) REVERT: B 163 ASP cc_start: 0.7362 (p0) cc_final: 0.6686 (m-30) REVERT: C 112 LYS cc_start: 0.4932 (mptt) cc_final: 0.4688 (mptt) REVERT: C 132 MET cc_start: 0.6248 (mmm) cc_final: 0.5505 (mpp) REVERT: C 135 MET cc_start: 0.4792 (mmm) cc_final: 0.4342 (tpp) REVERT: C 154 MET cc_start: 0.6984 (mmt) cc_final: 0.6388 (mmt) REVERT: D 82 THR cc_start: 0.7968 (p) cc_final: 0.7711 (p) REVERT: F 13 MET cc_start: 0.7801 (ppp) cc_final: 0.7416 (ppp) REVERT: F 17 ILE cc_start: 0.8682 (pt) cc_final: 0.8318 (pt) REVERT: F 59 MET cc_start: 0.8310 (mmp) cc_final: 0.8060 (mmt) REVERT: F 116 SER cc_start: 0.6308 (p) cc_final: 0.5945 (p) REVERT: F 162 TRP cc_start: 0.6492 (p90) cc_final: 0.6261 (p90) REVERT: G 89 ASP cc_start: 0.7904 (p0) cc_final: 0.6896 (t0) REVERT: G 238 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7671 (tttp) REVERT: J 538 MET cc_start: 0.7755 (ttt) cc_final: 0.7469 (ttt) REVERT: J 561 ILE cc_start: 0.9317 (tp) cc_final: 0.9093 (tt) REVERT: J 653 ILE cc_start: 0.7739 (mm) cc_final: 0.7350 (mm) REVERT: J 1217 ASP cc_start: 0.5668 (t70) cc_final: 0.5323 (t70) REVERT: J 1226 ARG cc_start: 0.6630 (mpp80) cc_final: 0.6406 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1463 time to fit residues: 73.4206 Evaluate side-chains 226 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 117 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 212 optimal weight: 6.9990 chunk 157 optimal weight: 0.0870 chunk 166 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN G 93 ASN G 243 ASN ** G 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.102082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.096729 restraints weight = 109203.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.096565 restraints weight = 135161.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.096687 restraints weight = 124049.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.096634 restraints weight = 93882.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.096680 restraints weight = 87819.833| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23369 Z= 0.124 Angle : 0.677 12.703 31823 Z= 0.351 Chirality : 0.047 0.214 3799 Planarity : 0.004 0.067 4159 Dihedral : 5.187 23.432 3449 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.24 % Favored : 87.54 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -3.20 (0.14), residues: 3235 helix: -0.14 (0.17), residues: 1010 sheet: -1.85 (0.23), residues: 476 loop : -3.62 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 528 TYR 0.022 0.001 TYR D 4 PHE 0.023 0.002 PHE G 221 TRP 0.035 0.002 TRP J 584 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00273 (23369) covalent geometry : angle 0.67666 (31823) hydrogen bonds : bond 0.03685 ( 761) hydrogen bonds : angle 5.04788 ( 2157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.29 seconds wall clock time: 71 minutes 36.39 seconds (4296.39 seconds total)