Starting phenix.real_space_refine on Sat Feb 17 14:45:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/02_2024/8sx8_40827_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/02_2024/8sx8_40827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/02_2024/8sx8_40827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/02_2024/8sx8_40827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/02_2024/8sx8_40827_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/02_2024/8sx8_40827_trim_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 6117 2.51 5 N 1580 2.21 5 O 1682 1.98 5 H 9610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 887": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 891": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 897": "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 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-5238/modules/chem_data/mon_lib" Total number of atoms: 19025 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 18997 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 1139} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'XPG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 8.99, per 1000 atoms: 0.47 Number of scatterers: 19025 At special positions: 0 Unit cell: (82.665, 96.86, 145.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 1682 8.00 N 1580 7.00 C 6117 6.00 H 9610 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: 19.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 65.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Proline residue: A 29 - end of helix 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 53 through 73 removed outlier: 3.689A pdb=" N GLU A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 6.434A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.617A pdb=" N GLU A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 104 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 106 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.707A pdb=" N ILE A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 180 removed outlier: 4.067A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 191 through 200 removed outlier: 3.766A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.941A pdb=" N ASP A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 288 removed outlier: 3.804A pdb=" N TRP A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.563A pdb=" N VAL A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 229 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 233 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY A 234 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 236 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.848A pdb=" N ILE A 254 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 262 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 269 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 283 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG A 284 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 286 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 341 removed outlier: 3.596A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.708A pdb=" N ALA A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 removed outlier: 3.553A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 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 551 Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 594 through 599 removed outlier: 4.782A 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: 3.842A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 807 removed outlier: 3.743A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 818 through 826 removed outlier: 4.202A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 835 through 860 removed outlier: 3.582A pdb=" N GLN A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 909 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 3.662A pdb=" N ARG A 879 " --> pdb=" O PHE A 876 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 890 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 895 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 898 " --> pdb=" O THR A 895 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 920 through 969 removed outlier: 3.606A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 1018 removed outlier: 4.122A pdb=" N THR A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 989 " --> pdb=" O TYR A 985 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.744A 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 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1131 through 1135 Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1156 through 1161 removed outlier: 4.760A pdb=" N ASP A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) 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 1211 through 1225 removed outlier: 3.665A pdb=" N ALA A1224 " --> pdb=" O ARG A1220 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS A1225 " --> pdb=" O GLU A1221 " (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: 4.240A pdb=" N GLN A1275 " --> pdb=" O LYS A1271 " (cutoff:3.500A) removed outlier: 3.827A 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 435 Processing sheet with id= B, first strand: chain 'A' and resid 610 through 614 removed outlier: 6.889A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A 443 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (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 1071 through 1075 removed outlier: 7.191A pdb=" N LYS A1243 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A1074 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET A1245 " --> pdb=" O VAL A1074 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A1248 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 6.424A pdb=" N THR A1227 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE A1200 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A1229 " --> pdb=" O ILE A1200 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1290 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: 7.10 Time building geometry restraints manager: 20.16 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: 9593 1.03 - 1.23: 24 1.23 - 1.42: 3988 1.42 - 1.61: 5562 1.61 - 1.81: 59 Bond restraints: 19226 Sorted by residual: bond pdb=" CB GLU A1202 " pdb=" HB2 GLU A1202 " ideal model delta sigma weight residual 0.970 1.091 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CG GLU A1202 " pdb=" HG3 GLU A1202 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CG GLU A1202 " pdb=" HG2 GLU A1202 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CB GLU A1202 " pdb=" HB3 GLU A1202 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C1 XPG A1401 " pdb=" O1A XPG A1401 " ideal model delta sigma weight residual 1.250 1.217 0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 19221 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.92: 450 106.92 - 113.78: 22855 113.78 - 120.63: 6808 120.63 - 127.49: 4584 127.49 - 134.35: 105 Bond angle restraints: 34802 Sorted by residual: angle pdb=" CA ARG A 951 " pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " ideal model delta sigma weight residual 114.10 107.28 6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C LEU A 181 " pdb=" N SER A 182 " pdb=" CA SER A 182 " ideal model delta sigma weight residual 120.71 125.30 -4.59 1.42e+00 4.96e-01 1.04e+01 angle pdb=" CA TYR A 985 " pdb=" CB TYR A 985 " pdb=" CG TYR A 985 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA HIS A 153 " pdb=" CB HIS A 153 " pdb=" CG HIS A 153 " ideal model delta sigma weight residual 113.80 110.70 3.10 1.00e+00 1.00e+00 9.58e+00 angle pdb=" CA PHE A 336 " pdb=" CB PHE A 336 " pdb=" CG PHE A 336 " ideal model delta sigma weight residual 113.80 110.80 3.00 1.00e+00 1.00e+00 9.00e+00 ... (remaining 34797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 8187 17.03 - 34.05: 457 34.05 - 51.08: 147 51.08 - 68.10: 160 68.10 - 85.13: 20 Dihedral angle restraints: 8971 sinusoidal: 4863 harmonic: 4108 Sorted by residual: dihedral pdb=" CA PRO A1094 " pdb=" C PRO A1094 " pdb=" N GLU A1095 " pdb=" CA GLU A1095 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLY A 282 " pdb=" C GLY A 282 " pdb=" N ILE A 283 " pdb=" CA ILE A 283 " ideal model delta harmonic sigma weight residual -180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ARG A1114 " pdb=" C ARG A1114 " pdb=" N LYS A1115 " pdb=" CA LYS A1115 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 8968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1013 0.049 - 0.099: 376 0.099 - 0.148: 91 0.148 - 0.197: 19 0.197 - 0.247: 7 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CA HIS A 153 " pdb=" N HIS A 153 " pdb=" C HIS A 153 " pdb=" CB HIS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C8 XPG A1401 " pdb=" C12 XPG A1401 " pdb=" C7 XPG A1401 " pdb=" C9 XPG A1401 " both_signs ideal model delta sigma weight residual False -2.54 -2.78 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA THR A 366 " pdb=" N THR A 366 " pdb=" C THR A 366 " pdb=" CB THR A 366 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1503 not shown) Planarity restraints: 2757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 216 " 0.035 2.00e-02 2.50e+03 3.43e-02 4.70e+01 pdb=" CG TRP A 216 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 216 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 216 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 216 " -0.096 2.00e-02 2.50e+03 pdb=" CE2 TRP A 216 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A 216 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 216 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 216 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 216 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP A 216 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 216 " 0.086 2.00e-02 2.50e+03 pdb=" HE3 TRP A 216 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 216 " 0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 216 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 216 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 994 " 0.042 2.00e-02 2.50e+03 5.12e-02 3.93e+01 pdb=" CD GLN A 994 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN A 994 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN A 994 " -0.080 2.00e-02 2.50e+03 pdb="HE21 GLN A 994 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN A 994 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 362 " -0.348 9.50e-02 1.11e+02 1.20e-01 3.71e+01 pdb=" NE ARG A 362 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 362 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 362 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 362 " 0.064 2.00e-02 2.50e+03 pdb="HH11 ARG A 362 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 362 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG A 362 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 362 " -0.068 2.00e-02 2.50e+03 ... (remaining 2754 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 797 2.16 - 2.77: 36514 2.77 - 3.38: 54086 3.38 - 3.99: 66208 3.99 - 4.60: 106537 Nonbonded interactions: 264142 Sorted by model distance: nonbonded pdb=" OD1 ASN A 544 " pdb="HH12 ARG A 547 " model vdw 1.545 1.850 nonbonded pdb=" HG SER A1051 " pdb=" OD1 ASP A1053 " model vdw 1.569 1.850 nonbonded pdb=" HG SER A1049 " pdb=" O PRO A1055 " model vdw 1.598 1.850 nonbonded pdb=" OE1 GLU A1020 " pdb=" H GLU A1020 " model vdw 1.598 1.850 nonbonded pdb=" HG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 1.602 1.850 ... (remaining 264137 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.330 Extract box with map and model: 6.950 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 67.530 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9616 Z= 0.320 Angle : 0.839 6.820 13029 Z= 0.507 Chirality : 0.056 0.247 1506 Planarity : 0.009 0.136 1621 Dihedral : 12.224 85.125 3524 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.10 % Allowed : 1.18 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.93 (0.21), residues: 1167 helix: -1.46 (0.15), residues: 767 sheet: -0.48 (0.49), residues: 73 loop : -0.40 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.006 TRP A 216 HIS 0.025 0.004 HIS A 153 PHE 0.031 0.004 PHE A 948 TYR 0.038 0.006 TYR A 155 ARG 0.014 0.003 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 112 ILE cc_start: 0.8362 (mm) cc_final: 0.8108 (mt) REVERT: A 276 MET cc_start: 0.7745 (mmm) cc_final: 0.7464 (mmt) REVERT: A 768 TYR cc_start: 0.7837 (t80) cc_final: 0.7488 (t80) REVERT: A 892 LEU cc_start: 0.8513 (tp) cc_final: 0.8278 (tp) REVERT: A 1007 MET cc_start: 0.8796 (mmm) cc_final: 0.7990 (mmm) REVERT: A 1083 SER cc_start: 0.8924 (m) cc_final: 0.8719 (p) REVERT: A 1256 ASP cc_start: 0.8679 (t0) cc_final: 0.8319 (t70) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.6486 time to fit residues: 148.0219 Evaluate side-chains 115 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN A 845 GLN A 999 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9616 Z= 0.227 Angle : 0.586 6.152 13029 Z= 0.325 Chirality : 0.039 0.157 1506 Planarity : 0.005 0.047 1621 Dihedral : 5.355 35.694 1304 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.08 % Allowed : 6.07 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.43 (0.23), residues: 1167 helix: -0.22 (0.18), residues: 754 sheet: -0.46 (0.53), residues: 63 loop : 0.02 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.008 0.002 HIS A 55 PHE 0.022 0.002 PHE A 324 TYR 0.012 0.001 TYR A 92 ARG 0.007 0.001 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7476 (tttp) cc_final: 0.7195 (mmtm) REVERT: A 112 ILE cc_start: 0.8172 (mm) cc_final: 0.7921 (mt) REVERT: A 1256 ASP cc_start: 0.8439 (t0) cc_final: 0.8092 (t70) outliers start: 11 outliers final: 9 residues processed: 129 average time/residue: 0.5751 time to fit residues: 100.6265 Evaluate side-chains 112 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9616 Z= 0.236 Angle : 0.533 5.432 13029 Z= 0.295 Chirality : 0.038 0.151 1506 Planarity : 0.004 0.045 1621 Dihedral : 5.147 37.832 1304 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.98 % Allowed : 7.05 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.06 (0.24), residues: 1167 helix: 0.04 (0.18), residues: 756 sheet: -1.13 (0.49), residues: 74 loop : 0.48 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.008 0.001 HIS A 153 PHE 0.021 0.002 PHE A 324 TYR 0.010 0.001 TYR A 917 ARG 0.006 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8184 (mm) cc_final: 0.7928 (mt) REVERT: A 1256 ASP cc_start: 0.8422 (t0) cc_final: 0.8054 (t70) outliers start: 10 outliers final: 8 residues processed: 114 average time/residue: 0.5321 time to fit residues: 83.4932 Evaluate side-chains 112 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 71 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9616 Z= 0.246 Angle : 0.519 5.156 13029 Z= 0.285 Chirality : 0.037 0.139 1506 Planarity : 0.004 0.044 1621 Dihedral : 4.960 35.481 1304 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.37 % Allowed : 7.74 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.18 (0.24), residues: 1167 helix: 0.24 (0.18), residues: 750 sheet: -1.06 (0.50), residues: 74 loop : 0.54 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.007 0.001 HIS A 152 PHE 0.020 0.002 PHE A 336 TYR 0.007 0.001 TYR A 728 ARG 0.007 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8417 (t0) cc_final: 0.8045 (t70) outliers start: 14 outliers final: 13 residues processed: 119 average time/residue: 0.5140 time to fit residues: 85.3455 Evaluate side-chains 114 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1183 GLN Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9616 Z= 0.313 Angle : 0.539 5.234 13029 Z= 0.298 Chirality : 0.038 0.150 1506 Planarity : 0.004 0.044 1621 Dihedral : 4.938 36.910 1304 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.27 % Allowed : 9.01 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.16 (0.24), residues: 1167 helix: 0.24 (0.18), residues: 744 sheet: -1.11 (0.51), residues: 74 loop : 0.51 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.008 0.002 HIS A 798 PHE 0.022 0.002 PHE A 336 TYR 0.008 0.001 TYR A 339 ARG 0.007 0.001 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8438 (t0) cc_final: 0.8104 (t70) outliers start: 13 outliers final: 12 residues processed: 116 average time/residue: 0.5186 time to fit residues: 84.3651 Evaluate side-chains 114 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1183 GLN Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 109 optimal weight: 0.0170 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9616 Z= 0.187 Angle : 0.479 4.832 13029 Z= 0.260 Chirality : 0.037 0.141 1506 Planarity : 0.003 0.041 1621 Dihedral : 4.751 37.843 1304 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.27 % Allowed : 8.91 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.61 (0.25), residues: 1167 helix: 0.58 (0.19), residues: 746 sheet: -1.02 (0.51), residues: 75 loop : 0.74 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 152 PHE 0.019 0.001 PHE A 336 TYR 0.009 0.001 TYR A1016 ARG 0.004 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 897 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8028 (ttm170) REVERT: A 1256 ASP cc_start: 0.8409 (t0) cc_final: 0.8073 (t70) outliers start: 13 outliers final: 11 residues processed: 114 average time/residue: 0.5290 time to fit residues: 84.4513 Evaluate side-chains 112 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1183 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9616 Z= 0.208 Angle : 0.480 4.846 13029 Z= 0.262 Chirality : 0.037 0.137 1506 Planarity : 0.003 0.040 1621 Dihedral : 4.690 40.334 1304 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.18 % Allowed : 9.11 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.68 (0.25), residues: 1167 helix: 0.64 (0.19), residues: 746 sheet: -0.87 (0.53), residues: 75 loop : 0.72 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.006 0.001 HIS A 798 PHE 0.019 0.001 PHE A 336 TYR 0.007 0.001 TYR A1016 ARG 0.003 0.000 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8422 (t0) cc_final: 0.8055 (t70) outliers start: 12 outliers final: 12 residues processed: 111 average time/residue: 0.5107 time to fit residues: 79.5876 Evaluate side-chains 113 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1183 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9616 Z= 0.178 Angle : 0.462 4.796 13029 Z= 0.251 Chirality : 0.036 0.166 1506 Planarity : 0.003 0.039 1621 Dihedral : 4.603 39.711 1304 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.47 % Allowed : 8.81 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1167 helix: 0.76 (0.19), residues: 746 sheet: -0.77 (0.53), residues: 75 loop : 0.75 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 152 PHE 0.019 0.001 PHE A 336 TYR 0.009 0.001 TYR A1016 ARG 0.002 0.000 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8417 (t0) cc_final: 0.8069 (t70) outliers start: 15 outliers final: 14 residues processed: 116 average time/residue: 0.5077 time to fit residues: 81.3877 Evaluate side-chains 117 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1183 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9616 Z= 0.212 Angle : 0.476 4.828 13029 Z= 0.260 Chirality : 0.037 0.145 1506 Planarity : 0.003 0.039 1621 Dihedral : 4.591 40.349 1304 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.57 % Allowed : 8.81 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.78 (0.25), residues: 1167 helix: 0.71 (0.19), residues: 752 sheet: -0.72 (0.53), residues: 75 loop : 0.73 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.006 0.001 HIS A 798 PHE 0.020 0.001 PHE A 336 TYR 0.007 0.001 TYR A1016 ARG 0.002 0.000 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8438 (t0) cc_final: 0.8111 (t70) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.5005 time to fit residues: 80.4782 Evaluate side-chains 116 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1183 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.0010 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 77 optimal weight: 0.0980 chunk 116 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 30.0000 chunk 73 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9616 Z= 0.127 Angle : 0.456 4.740 13029 Z= 0.243 Chirality : 0.036 0.154 1506 Planarity : 0.003 0.037 1621 Dihedral : 4.491 41.486 1304 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.98 % Allowed : 9.79 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1167 helix: 1.01 (0.20), residues: 752 sheet: -0.56 (0.53), residues: 75 loop : 0.96 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.004 0.001 HIS A 152 PHE 0.023 0.001 PHE A 948 TYR 0.011 0.001 TYR A1016 ARG 0.004 0.000 ARG A1114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7286 (tttp) cc_final: 0.7034 (mmtm) REVERT: A 1256 ASP cc_start: 0.8400 (t0) cc_final: 0.8083 (t70) outliers start: 10 outliers final: 9 residues processed: 115 average time/residue: 0.5160 time to fit residues: 82.8632 Evaluate side-chains 111 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1183 GLN Chi-restraints excluded: chain A residue 1199 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.174797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126248 restraints weight = 46056.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.126119 restraints weight = 21216.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.127540 restraints weight = 14945.304| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9616 Z= 0.162 Angle : 0.455 4.815 13029 Z= 0.245 Chirality : 0.036 0.139 1506 Planarity : 0.003 0.037 1621 Dihedral : 4.420 40.648 1304 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.88 % Allowed : 10.09 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1167 helix: 1.00 (0.19), residues: 752 sheet: -0.50 (0.54), residues: 75 loop : 0.96 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 153 PHE 0.021 0.001 PHE A 948 TYR 0.009 0.001 TYR A1016 ARG 0.002 0.000 ARG A 897 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.47 seconds wall clock time: 66 minutes 43.71 seconds (4003.71 seconds total)