Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 21:45:34 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/12_2021/5uar_8461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/12_2021/5uar_8461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/12_2021/5uar_8461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/12_2021/5uar_8461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/12_2021/5uar_8461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/12_2021/5uar_8461_updated.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.013 sd= 0.196 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 3": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 1038": "NH1" <-> "NH2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A ARG 1078": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9489 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9489 Unusual residues: {'D10': 2} Classifications: {'undetermined': 2, 'peptide': 1184} Link IDs: {'PTRANS': 39, 'TRANS': 1144, None: 2} Not linked: pdbres="HIS A1437 " pdbres="D10 A1501 " Not linked: pdbres="D10 A1501 " pdbres="D10 A1502 " Chain breaks: 4 Time building chain proxies: 5.39, per 1000 atoms: 0.57 Number of scatterers: 9489 At special positions: 0 Unit cell: (105, 122.64, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1672 8.00 N 1585 7.00 C 6177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 3.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 62.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.541A pdb=" N GLY A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 28 " --> pdb=" O MET A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.623A pdb=" N ARG A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.501A pdb=" N ARG A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 109 removed outlier: 3.884A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.784A pdb=" N ILE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.753A pdb=" N ALA A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Proline residue: A 141 - end of helix removed outlier: 3.732A pdb=" N HIS A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 4.065A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 174' Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.086A pdb=" N MET A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 215 removed outlier: 4.103A pdb=" N ASP A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N MET A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N HIS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.583A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 268 removed outlier: 3.560A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.735A pdb=" N GLN A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 281 through 327 removed outlier: 3.630A pdb=" N ILE A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.764A pdb=" N THR A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 347 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 376 removed outlier: 3.544A pdb=" N MET A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.610A pdb=" N ILE A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.564A pdb=" N ALA A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 549 through 562 removed outlier: 3.781A pdb=" N ARG A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.745A pdb=" N LYS A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 590 " --> pdb=" O PHE A 586 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 629 through 634 removed outlier: 3.567A pdb=" N SER A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 654 through 668 removed outlier: 3.718A pdb=" N HIS A 666 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 856 through 881 removed outlier: 3.710A pdb=" N LEU A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 864 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 890 removed outlier: 4.102A pdb=" N GLU A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 removed outlier: 3.715A pdb=" N ALA A 929 " --> pdb=" O TYR A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 934 No H-bonds generated for 'chain 'A' and resid 931 through 934' Processing helix chain 'A' and resid 939 through 965 Proline residue: A 944 - end of helix removed outlier: 3.578A pdb=" N HIS A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 951 " --> pdb=" O HIS A 947 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 952 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 958 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 985 removed outlier: 3.699A pdb=" N PHE A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 994 through 1019 removed outlier: 3.546A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A1000 " --> pdb=" O PRO A 996 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A1006 " --> pdb=" O PHE A1002 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1068 removed outlier: 4.204A pdb=" N THR A1028 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 3.546A pdb=" N ILE A1033 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A1035 " --> pdb=" O ILE A1032 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A1037 " --> pdb=" O PHE A1034 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A1042 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG A1043 " --> pdb=" O TYR A1040 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A1044 " --> pdb=" O PHE A1041 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN A1046 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A1047 " --> pdb=" O THR A1044 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1051 " --> pdb=" O LEU A1048 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A1054 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A1056 " --> pdb=" O THR A1053 " (cutoff:3.500A) Proline residue: A1058 - end of helix removed outlier: 3.841A pdb=" N HIS A1062 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A1064 " --> pdb=" O SER A1061 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A1065 " --> pdb=" O HIS A1062 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A1068 " --> pdb=" O MET A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.920A pdb=" N ARG A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1075 " --> pdb=" O TRP A1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1070 through 1075' Processing helix chain 'A' and resid 1079 through 1127 removed outlier: 3.729A pdb=" N HIS A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1090 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A1093 " --> pdb=" O THR A1089 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1115 " --> pdb=" O ALA A1111 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A1118 " --> pdb=" O LEU A1114 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1175 removed outlier: 3.719A pdb=" N CYS A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A1146 " --> pdb=" O CYS A1142 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A1148 " --> pdb=" O ALA A1144 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLY A1149 " --> pdb=" O MET A1145 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A1153 " --> pdb=" O GLY A1149 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A1162 " --> pdb=" O SER A1158 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A1166 " --> pdb=" O ASP A1162 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A1167 " --> pdb=" O GLY A1163 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A1169 " --> pdb=" O MET A1165 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1259 removed outlier: 4.175A pdb=" N PHE A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1284 Processing helix chain 'A' and resid 1301 through 1305 Processing helix chain 'A' and resid 1313 through 1323 Processing helix chain 'A' and resid 1327 through 1330 No H-bonds generated for 'chain 'A' and resid 1327 through 1330' Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 4.217A pdb=" N CYS A1356 " --> pdb=" O LYS A1352 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1376 No H-bonds generated for 'chain 'A' and resid 1374 through 1376' Processing helix chain 'A' and resid 1379 through 1392 removed outlier: 3.764A pdb=" N LYS A1383 " --> pdb=" O PRO A1379 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A1384 " --> pdb=" O VAL A1380 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A1390 " --> pdb=" O LYS A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1409 Processing helix chain 'A' and resid 1428 through 1431 No H-bonds generated for 'chain 'A' and resid 1428 through 1431' Processing sheet with id= A, first strand: chain 'A' and resid 599 through 601 removed outlier: 6.350A pdb=" N LYS A 614 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N THR A 456 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 616 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS A 619 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 4.228A pdb=" N SER A1413 " --> pdb=" O ARG A1240 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE A1398 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A1243 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A1400 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A1401 " --> pdb=" O LEU A1370 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1044 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: 2.80 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2933 1.35 - 1.48: 2373 1.48 - 1.61: 4295 1.61 - 1.73: 0 1.73 - 1.86: 93 Bond restraints: 9694 Sorted by residual: bond pdb=" CA ILE A 337 " pdb=" CB ILE A 337 " ideal model delta sigma weight residual 1.539 1.576 -0.037 1.13e-02 7.83e+03 1.06e+01 bond pdb=" N LEU A 995 " pdb=" CA LEU A 995 " ideal model delta sigma weight residual 1.463 1.482 -0.018 6.90e-03 2.10e+04 7.09e+00 bond pdb=" CA ARG A1020 " pdb=" C ARG A1020 " ideal model delta sigma weight residual 1.523 1.548 -0.026 1.00e-02 1.00e+04 6.53e+00 bond pdb=" N LEU A 189 " pdb=" CA LEU A 189 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.16e-02 7.43e+03 6.36e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.90e-02 2.77e+03 5.78e+00 ... (remaining 9689 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.08: 239 107.08 - 113.83: 5283 113.83 - 120.58: 3956 120.58 - 127.34: 3524 127.34 - 134.09: 93 Bond angle restraints: 13095 Sorted by residual: angle pdb=" N MET A 975 " pdb=" CA MET A 975 " pdb=" C MET A 975 " ideal model delta sigma weight residual 111.28 116.93 -5.65 1.09e+00 8.42e-01 2.69e+01 angle pdb=" N ASN A 188 " pdb=" CA ASN A 188 " pdb=" C ASN A 188 " ideal model delta sigma weight residual 112.23 118.67 -6.44 1.26e+00 6.30e-01 2.61e+01 angle pdb=" C ASP A1378 " pdb=" N PRO A1379 " pdb=" CA PRO A1379 " ideal model delta sigma weight residual 119.84 125.15 -5.31 1.25e+00 6.40e-01 1.80e+01 angle pdb=" N PHE A 110 " pdb=" CA PHE A 110 " pdb=" C PHE A 110 " ideal model delta sigma weight residual 108.52 115.42 -6.90 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N GLN A 39 " pdb=" CA GLN A 39 " pdb=" C GLN A 39 " ideal model delta sigma weight residual 110.33 115.69 -5.36 1.29e+00 6.01e-01 1.73e+01 ... (remaining 13090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5328 17.79 - 35.59: 385 35.59 - 53.38: 83 53.38 - 71.17: 12 71.17 - 88.97: 2 Dihedral angle restraints: 5810 sinusoidal: 2357 harmonic: 3453 Sorted by residual: dihedral pdb=" CA CYS A 77 " pdb=" C CYS A 77 " pdb=" N TYR A 78 " pdb=" CA TYR A 78 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP A 174 " pdb=" C ASP A 174 " pdb=" N LYS A 175 " pdb=" CA LYS A 175 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG A1284 " pdb=" C ARG A1284 " pdb=" N LYS A1285 " pdb=" CA LYS A1285 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1027 0.054 - 0.107: 352 0.107 - 0.161: 97 0.161 - 0.215: 22 0.215 - 0.268: 5 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CA THR A 977 " pdb=" N THR A 977 " pdb=" C THR A 977 " pdb=" CB THR A 977 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE A 201 " pdb=" N PHE A 201 " pdb=" C PHE A 201 " pdb=" CB PHE A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE A1296 " pdb=" N ILE A1296 " pdb=" C ILE A1296 " pdb=" CB ILE A1296 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1500 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 99 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 100 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1057 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO A1058 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 325 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.028 5.00e-02 4.00e+02 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3219 2.89 - 3.40: 9476 3.40 - 3.90: 14378 3.90 - 4.40: 15323 4.40 - 4.90: 26561 Nonbonded interactions: 68957 Sorted by model distance: nonbonded pdb=" O VAL A1384 " pdb=" OG1 THR A1388 " model vdw 2.393 2.440 nonbonded pdb=" O TYR A1220 " pdb=" OG1 THR A1221 " model vdw 2.508 2.440 nonbonded pdb=" O ASN A 10 " pdb=" OG SER A 13 " model vdw 2.539 2.440 nonbonded pdb=" O GLU A 293 " pdb=" OG1 THR A 297 " model vdw 2.558 2.440 nonbonded pdb=" O PHE A 945 " pdb=" OG1 THR A 949 " model vdw 2.564 2.440 ... (remaining 68952 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 6177 2.51 5 N 1585 2.21 5 O 1672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 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 Write .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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.530 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.090 Process input model: 26.710 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.140 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.054 9694 Z= 0.505 Angle : 1.182 8.467 13095 Z= 0.816 Chirality : 0.061 0.268 1503 Planarity : 0.004 0.053 1611 Dihedral : 13.303 88.968 3576 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.41 % Favored : 92.50 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.20), residues: 1174 helix: -2.16 (0.15), residues: 702 sheet: -2.76 (0.65), residues: 33 loop : -2.46 (0.28), residues: 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 350 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 358 average time/residue: 0.2157 time to fit residues: 105.7432 Evaluate side-chains 220 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0826 time to fit residues: 1.6674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.0670 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9694 Z= 0.236 Angle : 0.663 8.443 13095 Z= 0.340 Chirality : 0.041 0.190 1503 Planarity : 0.005 0.075 1611 Dihedral : 5.067 17.569 1295 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer Outliers : 4.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.61 (0.23), residues: 1174 helix: -0.35 (0.18), residues: 720 sheet: -2.29 (0.59), residues: 52 loop : -2.08 (0.30), residues: 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 240 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 260 average time/residue: 0.1915 time to fit residues: 72.0490 Evaluate side-chains 230 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0908 time to fit residues: 5.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.0570 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 620 ASN A1131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9694 Z= 0.171 Angle : 0.635 10.584 13095 Z= 0.311 Chirality : 0.040 0.174 1503 Planarity : 0.004 0.052 1611 Dihedral : 4.775 18.028 1295 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1174 helix: 0.21 (0.19), residues: 698 sheet: -1.72 (0.59), residues: 55 loop : -1.84 (0.29), residues: 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 248 average time/residue: 0.1973 time to fit residues: 69.7520 Evaluate side-chains 224 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0919 time to fit residues: 3.9785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9694 Z= 0.205 Angle : 0.611 9.208 13095 Z= 0.301 Chirality : 0.039 0.163 1503 Planarity : 0.005 0.139 1611 Dihedral : 4.670 18.500 1295 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1174 helix: 0.42 (0.19), residues: 704 sheet: -1.32 (0.60), residues: 50 loop : -1.78 (0.29), residues: 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 234 average time/residue: 0.1932 time to fit residues: 64.9852 Evaluate side-chains 215 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0895 time to fit residues: 4.3321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9694 Z= 0.154 Angle : 0.589 7.398 13095 Z= 0.290 Chirality : 0.039 0.183 1503 Planarity : 0.005 0.094 1611 Dihedral : 4.513 20.091 1295 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1174 helix: 0.52 (0.19), residues: 700 sheet: -1.01 (0.63), residues: 49 loop : -1.62 (0.29), residues: 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 222 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 228 average time/residue: 0.1952 time to fit residues: 64.6211 Evaluate side-chains 208 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0919 time to fit residues: 2.5662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 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 99 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9694 Z= 0.197 Angle : 0.619 7.765 13095 Z= 0.303 Chirality : 0.039 0.168 1503 Planarity : 0.005 0.110 1611 Dihedral : 4.570 23.739 1295 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1174 helix: 0.60 (0.19), residues: 695 sheet: -0.86 (0.62), residues: 55 loop : -1.61 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 225 average time/residue: 0.1909 time to fit residues: 63.2509 Evaluate side-chains 217 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0997 time to fit residues: 4.2418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9694 Z= 0.158 Angle : 0.602 7.809 13095 Z= 0.293 Chirality : 0.039 0.178 1503 Planarity : 0.005 0.092 1611 Dihedral : 4.420 19.996 1295 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1174 helix: 0.61 (0.20), residues: 699 sheet: -0.71 (0.63), residues: 61 loop : -1.61 (0.29), residues: 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 212 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 219 average time/residue: 0.1859 time to fit residues: 59.2253 Evaluate side-chains 204 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0923 time to fit residues: 2.5422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 0.0060 chunk 103 optimal weight: 0.0000 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9694 Z= 0.153 Angle : 0.621 8.854 13095 Z= 0.298 Chirality : 0.039 0.179 1503 Planarity : 0.004 0.085 1611 Dihedral : 4.397 26.594 1295 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1174 helix: 0.61 (0.20), residues: 699 sheet: -0.17 (0.68), residues: 55 loop : -1.61 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 215 average time/residue: 0.1944 time to fit residues: 60.6140 Evaluate side-chains 199 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0963 time to fit residues: 2.2388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 0.0870 chunk 100 optimal weight: 0.0000 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.9366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9694 Z= 0.179 Angle : 0.631 9.043 13095 Z= 0.304 Chirality : 0.040 0.179 1503 Planarity : 0.004 0.082 1611 Dihedral : 4.433 30.127 1295 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.24), residues: 1174 helix: 0.62 (0.19), residues: 702 sheet: -0.30 (0.68), residues: 57 loop : -1.59 (0.28), residues: 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 206 average time/residue: 0.1976 time to fit residues: 59.3428 Evaluate side-chains 200 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0903 time to fit residues: 2.7689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 99 optimal weight: 8.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9694 Z= 0.162 Angle : 0.632 9.511 13095 Z= 0.304 Chirality : 0.039 0.179 1503 Planarity : 0.004 0.081 1611 Dihedral : 4.429 31.772 1295 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.24), residues: 1174 helix: 0.59 (0.19), residues: 706 sheet: -0.37 (0.67), residues: 57 loop : -1.60 (0.28), residues: 411 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 201 average time/residue: 0.1923 time to fit residues: 56.4695 Evaluate side-chains 196 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0872 time to fit residues: 1.8791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 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 = 0.3854 r_free = 0.3854 target = 0.124031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102912 restraints weight = 25634.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105828 restraints weight = 13119.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107824 restraints weight = 8318.330| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3855 r_free = 0.3855 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9694 Z= 0.166 Angle : 0.647 9.596 13095 Z= 0.312 Chirality : 0.039 0.174 1503 Planarity : 0.004 0.079 1611 Dihedral : 4.390 31.098 1295 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.24), residues: 1174 helix: 0.67 (0.20), residues: 692 sheet: -0.33 (0.67), residues: 57 loop : -1.62 (0.28), residues: 425 =============================================================================== Job complete usr+sys time: 2126.40 seconds wall clock time: 40 minutes 15.00 seconds (2415.00 seconds total)