Starting phenix.real_space_refine on Wed Apr 10 04:08:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swn_40821/04_2024/8swn_40821_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swn_40821/04_2024/8swn_40821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swn_40821/04_2024/8swn_40821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swn_40821/04_2024/8swn_40821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swn_40821/04_2024/8swn_40821_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swn_40821/04_2024/8swn_40821_trim_updated.pdb" } resolution = 3.1 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= 0.003 sd= 0.075 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: 7 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5934 2.51 5 N 1529 2.21 5 O 1645 1.98 5 H 9269 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 284": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 384": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 436": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 503": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 571": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 587": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 782": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 807": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 820": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 824": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 879": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 880": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 915": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 922": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 946": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 951": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 998": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1012": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1030": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1076": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1090": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1234": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1295": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18422 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 18308 Classifications: {'peptide': 1135} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1100} Chain breaks: 4 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 2, 'ATP': 2, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 8.66, per 1000 atoms: 0.47 Number of scatterers: 18422 At special positions: 0 Unit cell: (72.558, 90.906, 147.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 P 7 15.00 Mg 2 11.99 O 1645 8.00 N 1529 7.00 C 5934 6.00 H 9269 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.60 Conformation dependent library (CDL) restraints added in 1.9 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 66.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.596A pdb=" N GLU A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 120 removed outlier: 5.817A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.526A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 180 removed outlier: 3.503A pdb=" N HIS A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 202 through 281 removed outlier: 3.952A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 209 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 212 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A 213 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 4.004A pdb=" N VAL A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 230 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE A 233 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY A 234 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 236 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 245 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.691A pdb=" N ILE A 254 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 256 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 259 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 261 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 263 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 274 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 292 through 341 removed outlier: 3.599A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 4.820A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 removed outlier: 3.998A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 537 through 550 removed outlier: 3.750A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 594 through 599 removed outlier: 4.825A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 711 through 744 removed outlier: 3.653A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 807 removed outlier: 3.747A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 815 Processing helix chain 'A' and resid 818 through 834 removed outlier: 3.904A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 Processing helix chain 'A' and resid 862 through 881 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 920 through 969 removed outlier: 3.755A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 976 through 987 Processing helix chain 'A' and resid 989 through 1018 removed outlier: 4.116A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.845A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1110 through 1116 removed outlier: 4.007A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1135 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1160 Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1172 through 1174 No H-bonds generated for 'chain 'A' and resid 1172 through 1174' Processing helix chain 'A' and resid 1179 through 1192 Processing helix chain 'A' and resid 1209 through 1222 removed outlier: 3.929A pdb=" N LEU A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.800A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1297 Processing sheet with id= A, first strand: chain 'A' and resid 433 through 436 removed outlier: 3.578A pdb=" N ILE A 409 " --> pdb=" O HIS A 472 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 610 through 614 removed outlier: 6.973A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL A 443 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY A 445 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= D, first strand: chain 'A' and resid 1251 through 1256 removed outlier: 6.807A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1419 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: 7.88 Time building geometry restraints manager: 16.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8227 1.03 - 1.23: 1128 1.23 - 1.43: 4018 1.43 - 1.62: 5182 1.62 - 1.82: 59 Bond restraints: 18614 Sorted by residual: bond pdb=" ND1 HIS A 158 " pdb=" CE1 HIS A 158 " ideal model delta sigma weight residual 1.321 1.235 0.086 1.00e-02 1.00e+04 7.42e+01 bond pdb=" N TYR A 358 " pdb=" H TYR A 358 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CE1 HIS A 158 " pdb=" HE1 HIS A 158 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ILE A 233 " pdb=" H ILE A 233 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 PHE A 211 " pdb=" HE1 PHE A 211 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 18609 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.65: 498 104.65 - 112.74: 20871 112.74 - 120.82: 8041 120.82 - 128.90: 4165 128.90 - 136.99: 93 Bond angle restraints: 33668 Sorted by residual: angle pdb=" PB ATP A1404 " pdb=" O3B ATP A1404 " pdb=" PG ATP A1404 " ideal model delta sigma weight residual 139.87 115.96 23.91 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP A1405 " pdb=" O3B ATP A1405 " pdb=" PG ATP A1405 " ideal model delta sigma weight residual 139.87 116.17 23.70 1.00e+00 1.00e+00 5.62e+02 angle pdb=" PA ATP A1404 " pdb=" O3A ATP A1404 " pdb=" PB ATP A1404 " ideal model delta sigma weight residual 136.83 113.83 23.00 1.00e+00 1.00e+00 5.29e+02 angle pdb=" PA ATP A1405 " pdb=" O3A ATP A1405 " pdb=" PB ATP A1405 " ideal model delta sigma weight residual 136.83 115.96 20.87 1.00e+00 1.00e+00 4.36e+02 angle pdb=" C5' ATP A1404 " pdb=" O5' ATP A1404 " pdb=" PA ATP A1404 " ideal model delta sigma weight residual 121.27 109.68 11.59 1.00e+00 1.00e+00 1.34e+02 ... (remaining 33663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 8142 21.63 - 43.25: 311 43.25 - 64.88: 223 64.88 - 86.50: 46 86.50 - 108.13: 2 Dihedral angle restraints: 8724 sinusoidal: 4769 harmonic: 3955 Sorted by residual: dihedral pdb=" CA ARG A 76 " pdb=" C ARG A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" C PHE A 156 " pdb=" N PHE A 156 " pdb=" CA PHE A 156 " pdb=" CB PHE A 156 " ideal model delta harmonic sigma weight residual -122.60 -137.50 14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA HIS A 55 " pdb=" C HIS A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 8721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1280 0.149 - 0.298: 17 0.298 - 0.447: 11 0.447 - 0.596: 92 0.596 - 0.745: 64 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CA PHE A 156 " pdb=" N PHE A 156 " pdb=" C PHE A 156 " pdb=" CB PHE A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CB VAL A 208 " pdb=" CA VAL A 208 " pdb=" CG1 VAL A 208 " pdb=" CG2 VAL A 208 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB ILE A 84 " pdb=" CA ILE A 84 " pdb=" CG1 ILE A 84 " pdb=" CG2 ILE A 84 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 1461 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 216 " -0.020 2.00e-02 2.50e+03 6.63e-02 1.76e+02 pdb=" CG TRP A 216 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 216 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 216 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP A 216 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP A 216 " 0.063 2.00e-02 2.50e+03 pdb=" CE3 TRP A 216 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 216 " 0.046 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 216 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 216 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TRP A 216 " 0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP A 216 " -0.210 2.00e-02 2.50e+03 pdb=" HE3 TRP A 216 " -0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 216 " 0.018 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 216 " -0.051 2.00e-02 2.50e+03 pdb=" HH2 TRP A 216 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 92 " 0.159 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG TYR A 92 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 92 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR A 92 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR A 92 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 92 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 92 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 92 " 0.130 2.00e-02 2.50e+03 pdb=" HD1 TYR A 92 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 TYR A 92 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 92 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 92 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1295 " -0.112 9.50e-02 1.11e+02 5.80e-02 4.57e+01 pdb=" NE ARG A1295 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A1295 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A1295 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A1295 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A1295 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A1295 " 0.075 2.00e-02 2.50e+03 pdb="HH21 ARG A1295 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG A1295 " -0.058 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 654 2.15 - 2.76: 34312 2.76 - 3.37: 52629 3.37 - 3.99: 67060 3.99 - 4.60: 106381 Nonbonded interactions: 261036 Sorted by model distance: nonbonded pdb=" OD2 ASP A 270 " pdb="HH22 ARG A 385 " model vdw 1.534 1.850 nonbonded pdb="HD21 ASN A 196 " pdb=" OD1 ASP A 270 " model vdw 1.597 1.850 nonbonded pdb=" OE1 GLU A 121 " pdb=" HG SER A 349 " model vdw 1.611 1.850 nonbonded pdb=" HG SER A 259 " pdb=" O13 PTY A1403 " model vdw 1.623 1.850 nonbonded pdb=" O ARG A 362 " pdb=" HG1 THR A 366 " model vdw 1.637 1.850 ... (remaining 261031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 1.630 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: 0.250 Extract box with map and model: 6.520 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 63.540 Find NCS groups from input model: 0.450 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.020 0.147 9345 Z= 1.289 Angle : 1.665 23.907 12669 Z= 1.142 Chirality : 0.202 0.745 1464 Planarity : 0.009 0.100 1559 Dihedral : 13.416 108.130 3463 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 7.93 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.67 (0.23), residues: 1125 helix: -0.66 (0.16), residues: 753 sheet: 0.41 (0.52), residues: 84 loop : 0.53 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP A 216 HIS 0.013 0.002 HIS A1233 PHE 0.034 0.004 PHE A 156 TYR 0.142 0.008 TYR A 92 ARG 0.026 0.002 ARG A1295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.503 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: A 241 MET cc_start: 0.7562 (tpp) cc_final: 0.7004 (tpt) REVERT: A 293 LYS cc_start: 0.8339 (mttm) cc_final: 0.7942 (ttpt) REVERT: A 1018 ASP cc_start: 0.8257 (m-30) cc_final: 0.8055 (t0) REVERT: A 1131 MET cc_start: 0.8564 (tpt) cc_final: 0.8243 (tpt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.7609 time to fit residues: 185.8861 Evaluate side-chains 104 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN A 742 GLN A 994 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9345 Z= 0.189 Angle : 0.547 5.373 12669 Z= 0.310 Chirality : 0.039 0.151 1464 Planarity : 0.004 0.036 1559 Dihedral : 9.960 91.850 1335 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.61 % Allowed : 4.58 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.67 (0.24), residues: 1125 helix: 0.58 (0.18), residues: 756 sheet: 0.01 (0.53), residues: 79 loop : 0.64 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 711 HIS 0.003 0.001 HIS A 152 PHE 0.011 0.001 PHE A 993 TYR 0.013 0.001 TYR A 768 ARG 0.006 0.001 ARG A1012 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7835 (mttt) cc_final: 0.7499 (tptt) REVERT: A 319 MET cc_start: 0.8774 (mmm) cc_final: 0.8169 (mmt) REVERT: A 1002 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7709 (mm-30) REVERT: A 1133 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7574 (tttt) outliers start: 6 outliers final: 3 residues processed: 118 average time/residue: 0.6571 time to fit residues: 102.1830 Evaluate side-chains 91 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 958 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9345 Z= 0.274 Angle : 0.523 5.303 12669 Z= 0.292 Chirality : 0.039 0.143 1464 Planarity : 0.004 0.037 1559 Dihedral : 9.367 89.456 1335 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.12 % Allowed : 5.49 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.83 (0.24), residues: 1125 helix: 0.82 (0.18), residues: 752 sheet: -0.25 (0.53), residues: 79 loop : 0.42 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 711 HIS 0.005 0.001 HIS A 710 PHE 0.015 0.001 PHE A 993 TYR 0.014 0.001 TYR A 737 ARG 0.005 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7926 (mttt) cc_final: 0.7586 (tptt) REVERT: A 292 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: A 509 LYS cc_start: 0.8650 (ptmt) cc_final: 0.8363 (ttpt) REVERT: A 580 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7772 (tp40) REVERT: A 833 ASP cc_start: 0.8148 (m-30) cc_final: 0.7743 (m-30) REVERT: A 1133 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7647 (tttt) outliers start: 11 outliers final: 6 residues processed: 101 average time/residue: 0.5617 time to fit residues: 77.4372 Evaluate side-chains 90 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9345 Z= 0.267 Angle : 0.494 5.408 12669 Z= 0.275 Chirality : 0.038 0.143 1464 Planarity : 0.004 0.042 1559 Dihedral : 9.145 88.217 1335 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.53 % Allowed : 5.80 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.95 (0.24), residues: 1125 helix: 0.94 (0.19), residues: 754 sheet: -0.24 (0.53), residues: 79 loop : 0.40 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 711 HIS 0.003 0.001 HIS A 592 PHE 0.010 0.001 PHE A 352 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7906 (mttt) cc_final: 0.7575 (tptt) REVERT: A 292 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: A 509 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8399 (ttpt) REVERT: A 580 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7808 (tp40) REVERT: A 833 ASP cc_start: 0.8219 (m-30) cc_final: 0.7823 (m-30) REVERT: A 994 GLN cc_start: 0.8310 (mt0) cc_final: 0.8091 (mt0) REVERT: A 1133 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7647 (tttt) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.6332 time to fit residues: 82.2197 Evaluate side-chains 93 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9345 Z= 0.167 Angle : 0.449 6.314 12669 Z= 0.248 Chirality : 0.037 0.142 1464 Planarity : 0.004 0.051 1559 Dihedral : 8.714 88.743 1335 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.02 % Allowed : 6.92 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.29 (0.25), residues: 1125 helix: 1.23 (0.19), residues: 752 sheet: -0.16 (0.53), residues: 79 loop : 0.46 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 711 HIS 0.003 0.001 HIS A 710 PHE 0.008 0.001 PHE A 352 TYR 0.008 0.001 TYR A 339 ARG 0.006 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7892 (mttt) cc_final: 0.7574 (tptt) REVERT: A 292 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: A 509 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8368 (ttpt) REVERT: A 527 MET cc_start: 0.8310 (mmm) cc_final: 0.8090 (mmt) REVERT: A 580 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7799 (tp40) REVERT: A 833 ASP cc_start: 0.8172 (m-30) cc_final: 0.7807 (m-30) REVERT: A 1133 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7646 (tttt) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 0.5746 time to fit residues: 75.1018 Evaluate side-chains 94 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9345 Z= 0.224 Angle : 0.461 5.263 12669 Z= 0.255 Chirality : 0.037 0.141 1464 Planarity : 0.004 0.041 1559 Dihedral : 8.554 83.952 1335 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.22 % Allowed : 6.92 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.30 (0.25), residues: 1125 helix: 1.24 (0.19), residues: 752 sheet: -0.04 (0.54), residues: 79 loop : 0.40 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 711 HIS 0.003 0.001 HIS A 710 PHE 0.010 0.001 PHE A 352 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7921 (mttt) cc_final: 0.7620 (tptt) REVERT: A 292 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 408 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7093 (mtt) REVERT: A 509 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8370 (ttpt) REVERT: A 527 MET cc_start: 0.8333 (mmm) cc_final: 0.8012 (mmt) REVERT: A 580 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7866 (tp40) REVERT: A 833 ASP cc_start: 0.8162 (m-30) cc_final: 0.7819 (m-30) REVERT: A 1133 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7625 (tttt) outliers start: 12 outliers final: 7 residues processed: 97 average time/residue: 0.6091 time to fit residues: 78.6779 Evaluate side-chains 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9345 Z= 0.200 Angle : 0.445 5.286 12669 Z= 0.246 Chirality : 0.037 0.155 1464 Planarity : 0.004 0.064 1559 Dihedral : 8.177 82.928 1335 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.22 % Allowed : 7.32 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.56 (0.25), residues: 1125 helix: 1.41 (0.19), residues: 745 sheet: 0.18 (0.58), residues: 69 loop : 0.56 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 711 HIS 0.003 0.001 HIS A 710 PHE 0.008 0.001 PHE A 352 TYR 0.009 0.001 TYR A 339 ARG 0.009 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7916 (mttt) cc_final: 0.7617 (tptt) REVERT: A 292 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 408 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.7046 (mtt) REVERT: A 509 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (ttpt) REVERT: A 527 MET cc_start: 0.8336 (mmm) cc_final: 0.8123 (mmt) REVERT: A 580 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7879 (tp40) REVERT: A 829 ILE cc_start: 0.8501 (mm) cc_final: 0.7688 (mm) REVERT: A 833 ASP cc_start: 0.8153 (m-30) cc_final: 0.7813 (m-30) REVERT: A 1133 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7620 (tttt) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.5904 time to fit residues: 74.3892 Evaluate side-chains 96 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9345 Z= 0.160 Angle : 0.429 4.901 12669 Z= 0.237 Chirality : 0.036 0.141 1464 Planarity : 0.004 0.056 1559 Dihedral : 7.774 80.511 1335 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 7.73 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.76 (0.25), residues: 1125 helix: 1.57 (0.19), residues: 745 sheet: 0.22 (0.58), residues: 69 loop : 0.64 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 711 HIS 0.003 0.001 HIS A 710 PHE 0.008 0.001 PHE A 352 TYR 0.008 0.001 TYR A 339 ARG 0.008 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7883 (mttt) cc_final: 0.7584 (tptt) REVERT: A 292 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: A 408 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7067 (mtt) REVERT: A 509 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8245 (ttpt) REVERT: A 527 MET cc_start: 0.8313 (mmm) cc_final: 0.8000 (mmt) REVERT: A 580 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: A 829 ILE cc_start: 0.8476 (mm) cc_final: 0.7608 (mm) REVERT: A 833 ASP cc_start: 0.8151 (m-30) cc_final: 0.7848 (m-30) REVERT: A 1133 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7602 (tttt) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.5994 time to fit residues: 77.4717 Evaluate side-chains 99 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 953 ASP Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9345 Z= 0.208 Angle : 0.446 5.110 12669 Z= 0.246 Chirality : 0.037 0.138 1464 Planarity : 0.004 0.060 1559 Dihedral : 7.824 79.427 1335 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.32 % Allowed : 7.63 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.67 (0.25), residues: 1125 helix: 1.49 (0.19), residues: 745 sheet: 0.27 (0.58), residues: 69 loop : 0.62 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.009 0.001 PHE A 352 TYR 0.010 0.001 TYR A 339 ARG 0.007 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7898 (mttt) cc_final: 0.7605 (tptt) REVERT: A 292 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: A 408 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.7037 (mtt) REVERT: A 509 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8247 (ttpt) REVERT: A 527 MET cc_start: 0.8322 (mmm) cc_final: 0.7987 (mmt) REVERT: A 580 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7900 (tp40) REVERT: A 833 ASP cc_start: 0.8164 (m-30) cc_final: 0.7820 (m-30) REVERT: A 1133 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7649 (tttt) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.5994 time to fit residues: 75.8564 Evaluate side-chains 97 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 953 ASP Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9345 Z= 0.186 Angle : 0.436 4.870 12669 Z= 0.241 Chirality : 0.036 0.140 1464 Planarity : 0.004 0.061 1559 Dihedral : 7.668 78.066 1335 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.22 % Allowed : 7.73 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.79 (0.25), residues: 1125 helix: 1.55 (0.19), residues: 744 sheet: 0.38 (0.59), residues: 69 loop : 0.72 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.009 0.001 PHE A 352 TYR 0.009 0.001 TYR A 339 ARG 0.008 0.000 ARG A 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.7894 (mttt) cc_final: 0.7609 (tptt) REVERT: A 292 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: A 408 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.7052 (mtt) REVERT: A 509 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8213 (ttpt) REVERT: A 527 MET cc_start: 0.8331 (mmm) cc_final: 0.8018 (mmt) REVERT: A 580 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7876 (tp40) REVERT: A 829 ILE cc_start: 0.8465 (mm) cc_final: 0.7618 (mm) REVERT: A 833 ASP cc_start: 0.8151 (m-30) cc_final: 0.7852 (m-30) REVERT: A 1133 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7626 (tttt) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.6457 time to fit residues: 77.7365 Evaluate side-chains 95 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 953 ASP Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095377 restraints weight = 35805.527| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.11 r_work: 0.2989 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9345 Z= 0.275 Angle : 0.469 5.174 12669 Z= 0.260 Chirality : 0.038 0.136 1464 Planarity : 0.004 0.061 1559 Dihedral : 7.956 79.320 1335 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.32 % Allowed : 7.63 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.57 (0.25), residues: 1125 helix: 1.37 (0.19), residues: 744 sheet: 0.39 (0.59), residues: 69 loop : 0.62 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.011 0.001 PHE A 352 TYR 0.011 0.001 TYR A 339 ARG 0.008 0.000 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4491.21 seconds wall clock time: 80 minutes 33.84 seconds (4833.84 seconds total)