Starting phenix.real_space_refine on Thu Feb 15 19:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebp_27995/02_2024/8ebp_27995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebp_27995/02_2024/8ebp_27995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebp_27995/02_2024/8ebp_27995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebp_27995/02_2024/8ebp_27995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebp_27995/02_2024/8ebp_27995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebp_27995/02_2024/8ebp_27995.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.062 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 70 5.16 5 C 8288 2.51 5 N 2278 2.21 5 O 2594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13230 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3320 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 15, 'TRANS': 419} Chain: "L" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1606 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1689 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3320 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 15, 'TRANS': 419} Chain: "M" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1606 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "I" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1689 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 12, 'TRANS': 212} Time building chain proxies: 6.87, per 1000 atoms: 0.52 Number of scatterers: 13230 At special positions: 0 Unit cell: (106.56, 103.23, 233.1, 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 70 16.00 O 2594 8.00 N 2278 7.00 C 8288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 212 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 212 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 2.5 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 36 sheets defined 17.9% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 65 through 92 removed outlier: 3.555A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.272A pdb=" N THR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.566A pdb=" N LEU A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 4.605A pdb=" N LYS A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 210 removed outlier: 3.557A pdb=" N GLN A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.613A pdb=" N ALA A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.609A pdb=" N ASP A 325 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.516A pdb=" N ILE A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.692A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.823A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 92 removed outlier: 3.527A pdb=" N LEU B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 removed outlier: 3.622A pdb=" N THR B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.559A pdb=" N LEU B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 173 removed outlier: 4.463A pdb=" N LYS B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 211 removed outlier: 3.655A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.786A pdb=" N ARG B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.699A pdb=" N ILE B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.641A pdb=" N ASP B 325 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.802A pdb=" N ILE B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 128 removed outlier: 3.783A pdb=" N ALA M 128 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 189 removed outlier: 3.791A pdb=" N HIS M 189 " --> pdb=" O GLN M 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.549A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.627A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.781A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LYS A 20 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.528A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 38 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.282A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.557A pdb=" N MET A 372 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.023A pdb=" N LYS A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.557A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.557A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB1, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.764A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU L 179 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR L 173 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.259A pdb=" N TRP L 149 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR L 146 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL L 196 " --> pdb=" O VAL L 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 192 through 193 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.666A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.152A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB7, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS H 140 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS H 140 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER H 180 " --> pdb=" O CYS H 140 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER H 177 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.598A pdb=" N LYS H 209 " --> pdb=" O CYS H 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.545A pdb=" N THR B 317 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS B 283 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 34 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS B 20 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.847A pdb=" N VAL B 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 38 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.739A pdb=" N THR B 45 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 158 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AC5, first strand: chain 'B' and resid 372 through 375 Processing sheet with id=AC6, first strand: chain 'B' and resid 401 through 402 removed outlier: 4.112A pdb=" N LYS B 401 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.447A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 9 through 13 Processing sheet with id=AC9, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.523A pdb=" N LEU M 179 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR M 173 " --> pdb=" O ASP M 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 145 through 148 removed outlier: 3.582A pdb=" N LYS M 205 " --> pdb=" O CYS M 194 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 150 through 151 Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.551A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.048A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 96 through 97 Processing sheet with id=AD7, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER I 180 " --> pdb=" O CYS I 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.587A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER I 180 " --> pdb=" O CYS I 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 195 through 198 removed outlier: 3.712A pdb=" N CYS I 196 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS I 209 " --> pdb=" O CYS I 196 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1284 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: 4.47 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4337 1.34 - 1.46: 2996 1.46 - 1.58: 6069 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 13490 Sorted by residual: bond pdb=" C ARG A 329 " pdb=" N GLY A 330 " ideal model delta sigma weight residual 1.331 1.291 0.039 1.46e-02 4.69e+03 7.19e+00 bond pdb=" C ARG B 329 " pdb=" N GLY B 330 " ideal model delta sigma weight residual 1.331 1.301 0.029 1.46e-02 4.69e+03 4.00e+00 bond pdb=" C TYR L 141 " pdb=" N PRO L 142 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.01e-02 9.80e+03 2.79e+00 bond pdb=" C ASP L 152 " pdb=" N SER L 153 " ideal model delta sigma weight residual 1.331 1.312 0.019 1.43e-02 4.89e+03 1.73e+00 bond pdb=" C PHE H 146 " pdb=" N PRO H 147 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.41e+00 ... (remaining 13485 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.84: 396 106.84 - 113.63: 7621 113.63 - 120.43: 4673 120.43 - 127.22: 5504 127.22 - 134.02: 142 Bond angle restraints: 18336 Sorted by residual: angle pdb=" N VAL B 52 " pdb=" CA VAL B 52 " pdb=" C VAL B 52 " ideal model delta sigma weight residual 113.53 108.44 5.09 9.80e-01 1.04e+00 2.70e+01 angle pdb=" C ASP L 152 " pdb=" CA ASP L 152 " pdb=" CB ASP L 152 " ideal model delta sigma weight residual 116.54 110.74 5.80 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 113.53 109.09 4.44 9.80e-01 1.04e+00 2.06e+01 angle pdb=" N SER L 153 " pdb=" CA SER L 153 " pdb=" C SER L 153 " ideal model delta sigma weight residual 113.02 118.24 -5.22 1.20e+00 6.94e-01 1.89e+01 angle pdb=" N PHE B 103 " pdb=" CA PHE B 103 " pdb=" C PHE B 103 " ideal model delta sigma weight residual 112.12 107.08 5.04 1.34e+00 5.57e-01 1.41e+01 ... (remaining 18331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7505 17.86 - 35.73: 583 35.73 - 53.59: 91 53.59 - 71.46: 16 71.46 - 89.32: 11 Dihedral angle restraints: 8206 sinusoidal: 3162 harmonic: 5044 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 339 " pdb=" CB CYS B 339 " ideal model delta sinusoidal sigma weight residual -86.00 -159.73 73.73 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 153.33 -60.33 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -145.72 59.72 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 8203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1573 0.045 - 0.090: 387 0.090 - 0.135: 140 0.135 - 0.181: 8 0.181 - 0.226: 6 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CB VAL B 104 " pdb=" CA VAL B 104 " pdb=" CG1 VAL B 104 " pdb=" CG2 VAL B 104 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP L 152 " pdb=" N ASP L 152 " pdb=" C ASP L 152 " pdb=" CB ASP L 152 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE H 100 " pdb=" CA ILE H 100 " pdb=" CG1 ILE H 100 " pdb=" CG2 ILE H 100 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2111 not shown) Planarity restraints: 2358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 184 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 185 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 152 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C ASP L 152 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP L 152 " 0.013 2.00e-02 2.50e+03 pdb=" N SER L 153 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 97 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO B 98 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.027 5.00e-02 4.00e+02 ... (remaining 2355 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 255 2.68 - 3.24: 12510 3.24 - 3.79: 19147 3.79 - 4.35: 25535 4.35 - 4.90: 43003 Nonbonded interactions: 100450 Sorted by model distance: nonbonded pdb=" OG SER B 391 " pdb=" OE1 GLN B 402 " model vdw 2.126 2.440 nonbonded pdb=" OG SER A 391 " pdb=" OE1 GLN A 402 " model vdw 2.159 2.440 nonbonded pdb=" O CYS B 60 " pdb=" NZ LYS B 68 " model vdw 2.187 2.520 nonbonded pdb=" OE2 GLU M 204 " pdb=" OG1 THR M 206 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR M 146 " pdb=" OG1 THR M 197 " model vdw 2.229 2.440 ... (remaining 100445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.260 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.004 0.048 13490 Z= 0.223 Angle : 0.632 8.063 18336 Z= 0.349 Chirality : 0.046 0.226 2114 Planarity : 0.004 0.051 2358 Dihedral : 12.803 89.323 4896 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1740 helix: -1.25 (0.30), residues: 277 sheet: 0.30 (0.24), residues: 537 loop : -2.02 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.008 0.001 HIS H 200 PHE 0.010 0.001 PHE H 100E TYR 0.013 0.001 TYR I 145 ARG 0.009 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8518 (mm) cc_final: 0.8276 (mm) REVERT: L 139 ASP cc_start: 0.9348 (m-30) cc_final: 0.9025 (m-30) REVERT: H 144 ASP cc_start: 0.8146 (m-30) cc_final: 0.7871 (m-30) REVERT: H 146 PHE cc_start: 0.8406 (t80) cc_final: 0.8199 (t80) REVERT: H 212 GLU cc_start: 0.7893 (pm20) cc_final: 0.7330 (tm-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2190 time to fit residues: 32.1478 Evaluate side-chains 67 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN H 199 ASN B 434 GLN M 79 GLN I 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13490 Z= 0.289 Angle : 0.650 9.767 18336 Z= 0.340 Chirality : 0.046 0.217 2114 Planarity : 0.004 0.055 2358 Dihedral : 4.267 18.048 1886 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.07 % Favored : 92.87 % Rotamer: Outliers : 0.27 % Allowed : 6.83 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1740 helix: -0.52 (0.33), residues: 269 sheet: 0.70 (0.24), residues: 534 loop : -2.07 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.008 0.001 HIS I 200 PHE 0.014 0.001 PHE H 100E TYR 0.039 0.001 TYR I 194 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8596 (mm) cc_final: 0.8349 (mm) REVERT: L 139 ASP cc_start: 0.9368 (m-30) cc_final: 0.8999 (m-30) REVERT: H 144 ASP cc_start: 0.8170 (m-30) cc_final: 0.7912 (m-30) REVERT: B 372 MET cc_start: 0.8484 (tmm) cc_final: 0.7857 (tmm) outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.2232 time to fit residues: 30.2264 Evaluate side-chains 72 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 392 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.2980 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 40.0000 chunk 139 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN H 155 ASN B 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13490 Z= 0.186 Angle : 0.570 6.608 18336 Z= 0.296 Chirality : 0.044 0.217 2114 Planarity : 0.004 0.056 2358 Dihedral : 4.135 18.251 1886 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.79 % Rotamer: Outliers : 0.88 % Allowed : 8.93 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1740 helix: -0.31 (0.33), residues: 272 sheet: 0.73 (0.23), residues: 553 loop : -2.01 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 149 HIS 0.008 0.001 HIS I 200 PHE 0.012 0.001 PHE H 100E TYR 0.021 0.001 TYR I 194 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.833 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8566 (mm) cc_final: 0.8335 (mm) REVERT: L 139 ASP cc_start: 0.9393 (m-30) cc_final: 0.9077 (m-30) REVERT: H 144 ASP cc_start: 0.8131 (m-30) cc_final: 0.7886 (m-30) REVERT: H 208 ASP cc_start: 0.9147 (m-30) cc_final: 0.8493 (t0) REVERT: H 212 GLU cc_start: 0.7791 (pm20) cc_final: 0.7288 (pp20) REVERT: M 141 TYR cc_start: 0.8754 (t80) cc_final: 0.8551 (t80) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.2210 time to fit residues: 31.8165 Evaluate side-chains 79 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.0270 chunk 117 optimal weight: 0.0970 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 40.0000 chunk 44 optimal weight: 0.0980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN H 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13490 Z= 0.146 Angle : 0.555 11.205 18336 Z= 0.287 Chirality : 0.043 0.221 2114 Planarity : 0.004 0.056 2358 Dihedral : 3.945 18.281 1886 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.74 % Allowed : 11.03 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1740 helix: -0.11 (0.34), residues: 271 sheet: 0.78 (0.23), residues: 576 loop : -1.90 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 154 HIS 0.008 0.001 HIS I 200 PHE 0.013 0.001 PHE M 62 TYR 0.017 0.001 TYR I 194 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8533 (mm) cc_final: 0.8322 (mm) REVERT: A 392 ILE cc_start: 0.8963 (mp) cc_final: 0.8699 (pt) REVERT: L 139 ASP cc_start: 0.9425 (m-30) cc_final: 0.9108 (m-30) REVERT: H 144 ASP cc_start: 0.7882 (m-30) cc_final: 0.7668 (m-30) REVERT: H 212 GLU cc_start: 0.7856 (pm20) cc_final: 0.7389 (pp20) REVERT: B 372 MET cc_start: 0.8419 (tmm) cc_final: 0.8201 (tmm) outliers start: 11 outliers final: 3 residues processed: 89 average time/residue: 0.2138 time to fit residues: 30.7792 Evaluate side-chains 73 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.0020 chunk 141 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 149 optimal weight: 40.0000 chunk 41 optimal weight: 0.8980 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13490 Z= 0.328 Angle : 0.610 6.730 18336 Z= 0.315 Chirality : 0.045 0.220 2114 Planarity : 0.004 0.058 2358 Dihedral : 4.137 18.309 1886 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 0.95 % Allowed : 12.92 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1740 helix: -0.11 (0.34), residues: 275 sheet: 0.66 (0.23), residues: 583 loop : -1.92 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.006 0.001 HIS I 200 PHE 0.015 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.008 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8618 (mm) cc_final: 0.8392 (mm) REVERT: L 139 ASP cc_start: 0.9391 (m-30) cc_final: 0.9120 (m-30) REVERT: H 144 ASP cc_start: 0.7897 (m-30) cc_final: 0.7672 (m-30) REVERT: H 212 GLU cc_start: 0.7849 (pm20) cc_final: 0.7389 (pp20) REVERT: B 372 MET cc_start: 0.8435 (tmm) cc_final: 0.8181 (tmm) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.2190 time to fit residues: 29.6305 Evaluate side-chains 75 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 189 HIS H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13490 Z= 0.181 Angle : 0.559 10.986 18336 Z= 0.289 Chirality : 0.044 0.220 2114 Planarity : 0.004 0.058 2358 Dihedral : 3.995 17.546 1886 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.51 % Rotamer: Outliers : 0.68 % Allowed : 14.55 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1740 helix: -0.00 (0.34), residues: 277 sheet: 0.84 (0.23), residues: 549 loop : -1.97 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.007 0.001 HIS I 200 PHE 0.013 0.001 PHE H 100E TYR 0.019 0.001 TYR M 141 ARG 0.003 0.000 ARG M 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8581 (mm) cc_final: 0.8379 (mm) REVERT: A 392 ILE cc_start: 0.8951 (mp) cc_final: 0.8705 (pt) REVERT: L 139 ASP cc_start: 0.9451 (m-30) cc_final: 0.9163 (m-30) REVERT: H 144 ASP cc_start: 0.7895 (m-30) cc_final: 0.7684 (m-30) REVERT: H 212 GLU cc_start: 0.7847 (pm20) cc_final: 0.7393 (pp20) REVERT: B 372 MET cc_start: 0.8427 (tmm) cc_final: 0.8159 (tmm) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.1933 time to fit residues: 26.1240 Evaluate side-chains 73 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain M residue 135 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 140 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13490 Z= 0.231 Angle : 0.568 10.437 18336 Z= 0.293 Chirality : 0.044 0.221 2114 Planarity : 0.004 0.057 2358 Dihedral : 3.988 17.747 1886 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 0.95 % Allowed : 14.82 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1740 helix: 0.04 (0.34), residues: 277 sheet: 0.68 (0.23), residues: 583 loop : -1.89 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.008 0.001 HIS I 200 PHE 0.014 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 95 ILE cc_start: 0.8592 (mm) cc_final: 0.8390 (mm) REVERT: A 392 ILE cc_start: 0.8897 (mp) cc_final: 0.8631 (tt) REVERT: L 139 ASP cc_start: 0.9439 (m-30) cc_final: 0.9157 (m-30) REVERT: H 212 GLU cc_start: 0.7845 (pm20) cc_final: 0.7395 (pp20) REVERT: B 372 MET cc_start: 0.8420 (tmm) cc_final: 0.8137 (tmm) REVERT: I 148 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8338 (mm-30) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.1946 time to fit residues: 27.7007 Evaluate side-chains 83 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13490 Z= 0.292 Angle : 0.593 9.673 18336 Z= 0.307 Chirality : 0.044 0.223 2114 Planarity : 0.004 0.057 2358 Dihedral : 4.069 18.345 1886 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 1.08 % Allowed : 15.29 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1740 helix: -0.05 (0.34), residues: 279 sheet: 0.63 (0.23), residues: 583 loop : -1.88 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.005 0.001 HIS H 200 PHE 0.015 0.001 PHE H 100E TYR 0.022 0.001 TYR M 141 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 392 ILE cc_start: 0.8902 (mp) cc_final: 0.8638 (tt) REVERT: L 139 ASP cc_start: 0.9454 (m-30) cc_final: 0.9181 (m-30) REVERT: B 372 MET cc_start: 0.8409 (tmm) cc_final: 0.7813 (tmm) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.2212 time to fit residues: 31.1752 Evaluate side-chains 81 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 0.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13490 Z= 0.162 Angle : 0.555 13.097 18336 Z= 0.285 Chirality : 0.043 0.226 2114 Planarity : 0.004 0.056 2358 Dihedral : 3.903 17.722 1886 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.51 % Rotamer: Outliers : 1.08 % Allowed : 15.36 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1740 helix: 0.14 (0.34), residues: 277 sheet: 0.73 (0.23), residues: 583 loop : -1.84 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 309 HIS 0.007 0.001 HIS I 200 PHE 0.012 0.001 PHE H 100E TYR 0.020 0.001 TYR M 141 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.624 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9104 (t) cc_final: 0.8808 (m) REVERT: A 392 ILE cc_start: 0.8877 (mp) cc_final: 0.8653 (tt) REVERT: L 139 ASP cc_start: 0.9444 (m-30) cc_final: 0.9164 (m-30) REVERT: H 34 MET cc_start: 0.8634 (mmm) cc_final: 0.8253 (mmt) REVERT: B 372 MET cc_start: 0.8373 (tmm) cc_final: 0.8088 (tmm) REVERT: I 87 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8386 (t) outliers start: 16 outliers final: 10 residues processed: 87 average time/residue: 0.1932 time to fit residues: 28.2899 Evaluate side-chains 83 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 chunk 14 optimal weight: 0.0170 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 108 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13490 Z= 0.174 Angle : 0.545 7.142 18336 Z= 0.280 Chirality : 0.043 0.227 2114 Planarity : 0.004 0.055 2358 Dihedral : 3.851 17.575 1886 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 0.88 % Allowed : 15.70 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1740 helix: 0.21 (0.34), residues: 277 sheet: 0.79 (0.23), residues: 578 loop : -1.78 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 309 HIS 0.008 0.001 HIS I 200 PHE 0.013 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.003 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9083 (t) cc_final: 0.8773 (m) REVERT: A 392 ILE cc_start: 0.8855 (mp) cc_final: 0.8632 (tt) REVERT: L 139 ASP cc_start: 0.9444 (m-30) cc_final: 0.9168 (m-30) REVERT: H 34 MET cc_start: 0.8659 (mmm) cc_final: 0.8258 (mmt) REVERT: B 372 MET cc_start: 0.8403 (tmm) cc_final: 0.8115 (tmm) REVERT: I 87 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8362 (t) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.1968 time to fit residues: 27.6733 Evaluate side-chains 83 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 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 = 0.3833 r_free = 0.3833 target = 0.103054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058232 restraints weight = 35510.382| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.09 r_work: 0.2702 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13490 Z= 0.187 Angle : 0.549 7.389 18336 Z= 0.282 Chirality : 0.043 0.229 2114 Planarity : 0.004 0.055 2358 Dihedral : 3.823 18.054 1886 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 1.15 % Allowed : 15.36 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1740 helix: 0.26 (0.34), residues: 278 sheet: 0.80 (0.23), residues: 578 loop : -1.75 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.006 0.001 HIS H 200 PHE 0.013 0.001 PHE H 100E TYR 0.021 0.001 TYR M 141 ARG 0.003 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.73 seconds wall clock time: 46 minutes 36.62 seconds (2796.62 seconds total)