Starting phenix.real_space_refine on Thu Mar 14 18:42:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/03_2024/5uar_8461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/03_2024/5uar_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_8461/03_2024/5uar_8461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/03_2024/5uar_8461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/03_2024/5uar_8461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uar_8461/03_2024/5uar_8461_updated.pdb" } resolution = 3.73 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= 0.013 sd= 0.196 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. 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-dev-5265/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: {'peptide': 1184, 'undetermined': 2} 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: 5.30, per 1000 atoms: 0.56 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 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 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: 2.43 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: 2.50 Time building geometry restraints manager: 3.64 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 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 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: 1.320 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: 0.000 Extract box with map and model: 7.170 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 26.870 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 % Allowed : 5.89 % Favored : 93.04 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 19 HIS 0.005 0.001 HIS A 114 PHE 0.015 0.001 PHE A 201 TYR 0.008 0.001 TYR A 248 ARG 0.007 0.001 ARG A1020 *********************** 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 : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8247 (mt-10) REVERT: A 11 CYS cc_start: 0.8537 (p) cc_final: 0.8184 (t) REVERT: A 12 LEU cc_start: 0.8953 (mp) cc_final: 0.8511 (tt) REVERT: A 52 ARG cc_start: 0.9218 (ttt180) cc_final: 0.8945 (mmm-85) REVERT: A 56 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8555 (mp0) REVERT: A 60 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8197 (mm-30) REVERT: A 70 LEU cc_start: 0.8466 (tp) cc_final: 0.8139 (tp) REVERT: A 93 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8930 (tp30) REVERT: A 122 TYR cc_start: 0.7951 (m-80) cc_final: 0.7691 (m-80) REVERT: A 207 LEU cc_start: 0.8795 (tp) cc_final: 0.8579 (tt) REVERT: A 288 ASN cc_start: 0.9142 (t0) cc_final: 0.8791 (m110) REVERT: A 296 LEU cc_start: 0.8215 (mt) cc_final: 0.7816 (tp) REVERT: A 336 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8409 (ttp-110) REVERT: A 463 LYS cc_start: 0.7512 (tttp) cc_final: 0.7017 (pttm) REVERT: A 509 LEU cc_start: 0.8964 (mt) cc_final: 0.8212 (tp) REVERT: A 631 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8107 (mp0) REVERT: A 633 GLN cc_start: 0.8168 (mt0) cc_final: 0.7697 (mm-40) REVERT: A 870 ILE cc_start: 0.8348 (mm) cc_final: 0.8064 (pt) REVERT: A 922 TYR cc_start: 0.8447 (p90) cc_final: 0.8133 (p90) REVERT: A 981 MET cc_start: 0.7524 (mmm) cc_final: 0.7323 (mmp) REVERT: A 1133 LYS cc_start: 0.9336 (pttt) cc_final: 0.9011 (pttt) REVERT: A 1170 ARG cc_start: 0.8416 (mmt90) cc_final: 0.7940 (mtm180) REVERT: A 1173 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8693 (mmtm) REVERT: A 1277 LYS cc_start: 0.8625 (mttt) cc_final: 0.8280 (ttmt) REVERT: A 1287 PHE cc_start: 0.8639 (m-80) cc_final: 0.8127 (m-80) REVERT: A 1313 ASP cc_start: 0.8725 (m-30) cc_final: 0.8062 (p0) REVERT: A 1334 ASP cc_start: 0.8369 (m-30) cc_final: 0.7997 (t0) REVERT: A 1337 ASP cc_start: 0.8910 (t70) cc_final: 0.8485 (m-30) REVERT: A 1366 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7776 (tmt170) REVERT: A 1423 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8177 (pttt) outliers start: 11 outliers final: 1 residues processed: 358 average time/residue: 0.2215 time to fit residues: 107.3749 Evaluate side-chains 230 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.0060 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 620 ASN ** A1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9694 Z= 0.239 Angle : 0.659 8.741 13095 Z= 0.337 Chirality : 0.042 0.177 1503 Planarity : 0.004 0.040 1611 Dihedral : 5.192 36.717 1297 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 4.15 % Allowed : 14.78 % Favored : 81.06 % 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: -1.54 (0.23), residues: 1174 helix: -0.29 (0.18), residues: 722 sheet: -2.36 (0.58), residues: 52 loop : -2.07 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1106 HIS 0.005 0.001 HIS A1311 PHE 0.016 0.002 PHE A 940 TYR 0.017 0.002 TYR A1263 ARG 0.004 0.001 ARG A 515 *********************** 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 286 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 CYS cc_start: 0.8696 (p) cc_final: 0.8403 (t) REVERT: A 12 LEU cc_start: 0.8848 (mp) cc_final: 0.8442 (tt) REVERT: A 24 MET cc_start: 0.8937 (tpp) cc_final: 0.8498 (mmm) REVERT: A 60 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8508 (mm-30) REVERT: A 93 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9022 (tp30) REVERT: A 122 TYR cc_start: 0.7913 (m-80) cc_final: 0.7578 (m-80) REVERT: A 135 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7508 (ttm110) REVERT: A 207 LEU cc_start: 0.8812 (tp) cc_final: 0.8553 (tt) REVERT: A 245 MET cc_start: 0.9028 (mmm) cc_final: 0.8825 (mmm) REVERT: A 288 ASN cc_start: 0.9134 (t0) cc_final: 0.8809 (m110) REVERT: A 366 MET cc_start: 0.7955 (mmm) cc_final: 0.7739 (tmm) REVERT: A 379 GLU cc_start: 0.8569 (tp30) cc_final: 0.8282 (tp30) REVERT: A 386 TYR cc_start: 0.6862 (p90) cc_final: 0.6208 (p90) REVERT: A 388 LEU cc_start: 0.9031 (mt) cc_final: 0.8428 (mp) REVERT: A 399 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8633 (p) REVERT: A 463 LYS cc_start: 0.7603 (tttp) cc_final: 0.7088 (pttp) REVERT: A 509 LEU cc_start: 0.8797 (mt) cc_final: 0.8151 (tp) REVERT: A 1170 ARG cc_start: 0.8327 (mmt90) cc_final: 0.8000 (mtm180) REVERT: A 1220 TYR cc_start: 0.6447 (t80) cc_final: 0.5848 (t80) REVERT: A 1277 LYS cc_start: 0.8706 (mttt) cc_final: 0.8339 (ttmt) REVERT: A 1278 MET cc_start: 0.7898 (mtt) cc_final: 0.7365 (mtt) REVERT: A 1313 ASP cc_start: 0.8781 (m-30) cc_final: 0.8202 (p0) REVERT: A 1334 ASP cc_start: 0.8355 (m-30) cc_final: 0.7827 (t0) REVERT: A 1366 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7754 (ttt180) REVERT: A 1370 LEU cc_start: 0.7900 (mt) cc_final: 0.7694 (tp) outliers start: 43 outliers final: 21 residues processed: 266 average time/residue: 0.2013 time to fit residues: 74.7934 Evaluate side-chains 224 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9694 Z= 0.192 Angle : 0.603 8.650 13095 Z= 0.303 Chirality : 0.039 0.172 1503 Planarity : 0.004 0.047 1611 Dihedral : 4.903 36.794 1297 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.15 % Allowed : 19.13 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1174 helix: 0.25 (0.19), residues: 714 sheet: -1.71 (0.62), residues: 52 loop : -1.86 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1153 HIS 0.004 0.001 HIS A1311 PHE 0.013 0.001 PHE A 940 TYR 0.011 0.001 TYR A 38 ARG 0.005 0.000 ARG A 336 *********************** 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 272 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8385 (ppp) cc_final: 0.8114 (ppp) REVERT: A 11 CYS cc_start: 0.8628 (p) cc_final: 0.8403 (t) REVERT: A 12 LEU cc_start: 0.8839 (mp) cc_final: 0.8424 (tt) REVERT: A 24 MET cc_start: 0.8972 (tpp) cc_final: 0.7832 (ttm) REVERT: A 43 GLN cc_start: 0.8585 (tp40) cc_final: 0.8135 (tp-100) REVERT: A 60 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8517 (mm-30) REVERT: A 93 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8899 (tp30) REVERT: A 122 TYR cc_start: 0.7941 (m-80) cc_final: 0.7358 (m-80) REVERT: A 123 PHE cc_start: 0.7770 (m-10) cc_final: 0.6200 (t80) REVERT: A 135 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7511 (ttm110) REVERT: A 171 ARG cc_start: 0.9252 (mtm180) cc_final: 0.8590 (ttt180) REVERT: A 245 MET cc_start: 0.8998 (mmm) cc_final: 0.8783 (mmm) REVERT: A 288 ASN cc_start: 0.9141 (t0) cc_final: 0.8816 (m110) REVERT: A 344 CYS cc_start: 0.8905 (m) cc_final: 0.8643 (t) REVERT: A 366 MET cc_start: 0.8006 (mmm) cc_final: 0.7782 (tmm) REVERT: A 379 GLU cc_start: 0.8788 (tp30) cc_final: 0.8398 (tp30) REVERT: A 388 LEU cc_start: 0.9038 (mt) cc_final: 0.8441 (mp) REVERT: A 463 LYS cc_start: 0.7590 (tttp) cc_final: 0.7047 (pttp) REVERT: A 509 LEU cc_start: 0.8824 (mt) cc_final: 0.8103 (tp) REVERT: A 960 MET cc_start: 0.8824 (ttt) cc_final: 0.8008 (tmm) REVERT: A 1004 GLN cc_start: 0.8481 (tp40) cc_final: 0.8213 (tp40) REVERT: A 1040 TYR cc_start: 0.8647 (t80) cc_final: 0.8226 (t80) REVERT: A 1112 ASP cc_start: 0.8338 (t0) cc_final: 0.8078 (t0) REVERT: A 1133 LYS cc_start: 0.9206 (pttt) cc_final: 0.8686 (ptmt) REVERT: A 1170 ARG cc_start: 0.8358 (mmt90) cc_final: 0.7959 (mtm180) REVERT: A 1220 TYR cc_start: 0.6410 (t80) cc_final: 0.5664 (t80) REVERT: A 1227 VAL cc_start: 0.7398 (t) cc_final: 0.7028 (m) REVERT: A 1277 LYS cc_start: 0.8742 (mttt) cc_final: 0.8345 (ttmt) REVERT: A 1278 MET cc_start: 0.7930 (mtt) cc_final: 0.7336 (ttm) REVERT: A 1313 ASP cc_start: 0.8791 (m-30) cc_final: 0.8205 (p0) REVERT: A 1334 ASP cc_start: 0.8267 (m-30) cc_final: 0.7769 (t0) REVERT: A 1366 ARG cc_start: 0.8152 (ttt180) cc_final: 0.7705 (ttt180) REVERT: A 1367 ILE cc_start: 0.8925 (mm) cc_final: 0.8604 (mm) REVERT: A 1370 LEU cc_start: 0.8010 (mt) cc_final: 0.7791 (tp) outliers start: 43 outliers final: 31 residues processed: 253 average time/residue: 0.2025 time to fit residues: 71.9954 Evaluate side-chains 233 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.0070 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1046 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9694 Z= 0.164 Angle : 0.575 7.647 13095 Z= 0.284 Chirality : 0.039 0.162 1503 Planarity : 0.004 0.055 1611 Dihedral : 4.717 37.171 1297 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.25 % Allowed : 19.90 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.24), residues: 1174 helix: 0.60 (0.20), residues: 697 sheet: -1.27 (0.61), residues: 55 loop : -1.65 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1153 HIS 0.004 0.001 HIS A1311 PHE 0.024 0.001 PHE A 863 TYR 0.013 0.001 TYR A 927 ARG 0.004 0.000 ARG A 336 *********************** 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 266 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8356 (ppp) cc_final: 0.8036 (ppp) REVERT: A 11 CYS cc_start: 0.8610 (p) cc_final: 0.8408 (t) REVERT: A 12 LEU cc_start: 0.8826 (mp) cc_final: 0.8411 (tt) REVERT: A 24 MET cc_start: 0.8970 (tpp) cc_final: 0.7507 (ttm) REVERT: A 33 ARG cc_start: 0.8625 (mtt180) cc_final: 0.7751 (ptp90) REVERT: A 43 GLN cc_start: 0.8616 (tp40) cc_final: 0.8165 (tp-100) REVERT: A 60 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 93 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8942 (tp30) REVERT: A 122 TYR cc_start: 0.7826 (m-80) cc_final: 0.7358 (m-80) REVERT: A 123 PHE cc_start: 0.7791 (m-10) cc_final: 0.6267 (t80) REVERT: A 135 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7570 (ttm110) REVERT: A 245 MET cc_start: 0.8965 (mmm) cc_final: 0.8727 (mmm) REVERT: A 288 ASN cc_start: 0.9117 (t0) cc_final: 0.8808 (m110) REVERT: A 344 CYS cc_start: 0.8864 (m) cc_final: 0.8604 (t) REVERT: A 361 MET cc_start: 0.7222 (tmm) cc_final: 0.6899 (tmm) REVERT: A 388 LEU cc_start: 0.8996 (mt) cc_final: 0.8433 (mp) REVERT: A 509 LEU cc_start: 0.8804 (mt) cc_final: 0.8021 (tp) REVERT: A 631 GLU cc_start: 0.8728 (mp0) cc_final: 0.8213 (pt0) REVERT: A 635 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8241 (mm-30) REVERT: A 655 GLU cc_start: 0.7547 (pt0) cc_final: 0.6819 (tm-30) REVERT: A 849 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8305 (mtp180) REVERT: A 922 TYR cc_start: 0.8528 (p90) cc_final: 0.8283 (p90) REVERT: A 960 MET cc_start: 0.8764 (ttt) cc_final: 0.8010 (tmm) REVERT: A 1004 GLN cc_start: 0.8399 (tp40) cc_final: 0.8112 (tp40) REVERT: A 1040 TYR cc_start: 0.8667 (t80) cc_final: 0.7978 (t80) REVERT: A 1133 LYS cc_start: 0.9179 (pttt) cc_final: 0.8662 (ptmt) REVERT: A 1170 ARG cc_start: 0.8434 (mmt90) cc_final: 0.8024 (mtm180) REVERT: A 1220 TYR cc_start: 0.6298 (t80) cc_final: 0.5490 (t80) REVERT: A 1278 MET cc_start: 0.7925 (mtt) cc_final: 0.7423 (ttm) REVERT: A 1334 ASP cc_start: 0.8248 (m-30) cc_final: 0.7750 (t0) REVERT: A 1341 GLU cc_start: 0.8198 (mp0) cc_final: 0.7868 (mp0) REVERT: A 1370 LEU cc_start: 0.8074 (mt) cc_final: 0.7863 (tp) REVERT: A 1416 MET cc_start: 0.5565 (ttt) cc_final: 0.4935 (ttm) REVERT: A 1417 MET cc_start: 0.7199 (tmm) cc_final: 0.6773 (tmm) outliers start: 44 outliers final: 34 residues processed: 247 average time/residue: 0.1916 time to fit residues: 67.4093 Evaluate side-chains 242 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.0570 chunk 97 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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: 0.7697 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9694 Z= 0.141 Angle : 0.545 8.466 13095 Z= 0.268 Chirality : 0.038 0.169 1503 Planarity : 0.004 0.050 1611 Dihedral : 4.449 36.610 1297 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.15 % Allowed : 20.48 % Favored : 75.36 % 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: -0.27 (0.24), residues: 1174 helix: 0.82 (0.20), residues: 698 sheet: -0.86 (0.66), residues: 54 loop : -1.76 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1153 HIS 0.003 0.000 HIS A1311 PHE 0.013 0.001 PHE A 940 TYR 0.007 0.001 TYR A1263 ARG 0.005 0.000 ARG A 486 *********************** 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 276 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8341 (ppp) cc_final: 0.7988 (ppp) REVERT: A 11 CYS cc_start: 0.8631 (p) cc_final: 0.8415 (t) REVERT: A 12 LEU cc_start: 0.8833 (mp) cc_final: 0.8423 (tt) REVERT: A 24 MET cc_start: 0.8921 (tpp) cc_final: 0.7930 (ttm) REVERT: A 33 ARG cc_start: 0.8554 (mtt180) cc_final: 0.7641 (ptp90) REVERT: A 43 GLN cc_start: 0.8645 (tp40) cc_final: 0.8217 (tp-100) REVERT: A 60 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8427 (mm-30) REVERT: A 93 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9076 (tp30) REVERT: A 122 TYR cc_start: 0.7676 (m-80) cc_final: 0.7138 (m-80) REVERT: A 123 PHE cc_start: 0.7649 (m-10) cc_final: 0.6261 (t80) REVERT: A 135 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7467 (ttm110) REVERT: A 171 ARG cc_start: 0.8917 (mtm180) cc_final: 0.8251 (ttt180) REVERT: A 245 MET cc_start: 0.8960 (mmm) cc_final: 0.8726 (mmm) REVERT: A 288 ASN cc_start: 0.9144 (t0) cc_final: 0.8829 (m110) REVERT: A 344 CYS cc_start: 0.8849 (m) cc_final: 0.8609 (t) REVERT: A 361 MET cc_start: 0.7224 (tmm) cc_final: 0.6920 (tmm) REVERT: A 379 GLU cc_start: 0.8867 (tp30) cc_final: 0.8583 (tp30) REVERT: A 384 MET cc_start: 0.8012 (tmm) cc_final: 0.7744 (tmm) REVERT: A 388 LEU cc_start: 0.8972 (mt) cc_final: 0.8404 (mp) REVERT: A 631 GLU cc_start: 0.8685 (mp0) cc_final: 0.8173 (pt0) REVERT: A 635 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: A 655 GLU cc_start: 0.7579 (pt0) cc_final: 0.6851 (tm-30) REVERT: A 849 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8308 (mtp180) REVERT: A 922 TYR cc_start: 0.8430 (p90) cc_final: 0.7765 (p90) REVERT: A 960 MET cc_start: 0.8667 (ttt) cc_final: 0.7951 (tmm) REVERT: A 1004 GLN cc_start: 0.8361 (tp40) cc_final: 0.8064 (tp40) REVERT: A 1077 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8784 (pm20) REVERT: A 1133 LYS cc_start: 0.9147 (pttt) cc_final: 0.8886 (pttm) REVERT: A 1143 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7269 (tp) REVERT: A 1170 ARG cc_start: 0.8399 (mmt90) cc_final: 0.7984 (mtm180) REVERT: A 1278 MET cc_start: 0.7823 (mtt) cc_final: 0.7364 (ttm) REVERT: A 1334 ASP cc_start: 0.8265 (m-30) cc_final: 0.7764 (t0) REVERT: A 1386 LYS cc_start: 0.9053 (mttm) cc_final: 0.8458 (tppt) REVERT: A 1416 MET cc_start: 0.5457 (ttt) cc_final: 0.4965 (ttm) REVERT: A 1417 MET cc_start: 0.7215 (tmm) cc_final: 0.6948 (tmm) outliers start: 43 outliers final: 27 residues processed: 253 average time/residue: 0.1899 time to fit residues: 68.1363 Evaluate side-chains 240 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9694 Z= 0.183 Angle : 0.564 6.583 13095 Z= 0.278 Chirality : 0.039 0.166 1503 Planarity : 0.004 0.052 1611 Dihedral : 4.454 37.432 1297 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.25 % Allowed : 21.93 % Favored : 73.82 % 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: -0.10 (0.24), residues: 1174 helix: 0.86 (0.20), residues: 700 sheet: -0.46 (0.71), residues: 48 loop : -1.57 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1153 HIS 0.004 0.001 HIS A1311 PHE 0.027 0.001 PHE A 863 TYR 0.015 0.001 TYR A1342 ARG 0.003 0.000 ARG A 105 *********************** 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 265 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8445 (ppp) cc_final: 0.8083 (ppp) REVERT: A 11 CYS cc_start: 0.8679 (p) cc_final: 0.8477 (t) REVERT: A 12 LEU cc_start: 0.8895 (mp) cc_final: 0.8500 (tt) REVERT: A 24 MET cc_start: 0.8953 (tpp) cc_final: 0.8168 (mtt) REVERT: A 33 ARG cc_start: 0.8594 (mtt180) cc_final: 0.7694 (ptp90) REVERT: A 43 GLN cc_start: 0.8647 (tp40) cc_final: 0.8246 (tp-100) REVERT: A 60 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 93 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8969 (tp30) REVERT: A 122 TYR cc_start: 0.7875 (m-80) cc_final: 0.7434 (m-80) REVERT: A 123 PHE cc_start: 0.7658 (m-10) cc_final: 0.6329 (t80) REVERT: A 135 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7496 (ttm110) REVERT: A 171 ARG cc_start: 0.8908 (mtm180) cc_final: 0.8303 (ttt180) REVERT: A 245 MET cc_start: 0.8938 (mmm) cc_final: 0.8573 (mmm) REVERT: A 288 ASN cc_start: 0.9076 (t0) cc_final: 0.8779 (m110) REVERT: A 361 MET cc_start: 0.7397 (tmm) cc_final: 0.7066 (tmm) REVERT: A 388 LEU cc_start: 0.8986 (mt) cc_final: 0.8419 (mp) REVERT: A 631 GLU cc_start: 0.8721 (mp0) cc_final: 0.8343 (pt0) REVERT: A 635 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: A 655 GLU cc_start: 0.7530 (pt0) cc_final: 0.6733 (tm-30) REVERT: A 849 ARG cc_start: 0.8647 (mtt180) cc_final: 0.8324 (mtp180) REVERT: A 960 MET cc_start: 0.8691 (ttt) cc_final: 0.7934 (tmm) REVERT: A 994 MET cc_start: 0.7647 (mmm) cc_final: 0.7352 (mtp) REVERT: A 1040 TYR cc_start: 0.8719 (t80) cc_final: 0.8340 (t80) REVERT: A 1077 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8819 (mp0) REVERT: A 1133 LYS cc_start: 0.9195 (pttt) cc_final: 0.8711 (ptmt) REVERT: A 1170 ARG cc_start: 0.8374 (mmt90) cc_final: 0.7928 (mtm180) REVERT: A 1280 LEU cc_start: 0.9092 (mm) cc_final: 0.8891 (mm) REVERT: A 1281 GLN cc_start: 0.9121 (pm20) cc_final: 0.8606 (pm20) REVERT: A 1282 LYS cc_start: 0.9313 (ptmt) cc_final: 0.9013 (pttt) REVERT: A 1334 ASP cc_start: 0.8222 (m-30) cc_final: 0.7727 (t0) REVERT: A 1386 LYS cc_start: 0.9094 (mttm) cc_final: 0.8512 (tppt) REVERT: A 1416 MET cc_start: 0.5360 (ttt) cc_final: 0.4913 (ttm) outliers start: 44 outliers final: 31 residues processed: 246 average time/residue: 0.1912 time to fit residues: 66.8161 Evaluate side-chains 248 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 215 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU 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: 2.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9694 Z= 0.178 Angle : 0.581 9.419 13095 Z= 0.285 Chirality : 0.039 0.188 1503 Planarity : 0.004 0.051 1611 Dihedral : 4.464 37.611 1297 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.86 % Allowed : 23.96 % Favored : 72.17 % 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: -0.13 (0.25), residues: 1174 helix: 0.80 (0.20), residues: 700 sheet: -0.65 (0.67), residues: 54 loop : -1.49 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 887 HIS 0.004 0.001 HIS A1311 PHE 0.033 0.001 PHE A 863 TYR 0.023 0.001 TYR A1342 ARG 0.003 0.000 ARG A 105 *********************** 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 257 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 217 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8503 (ppp) cc_final: 0.8141 (ppp) REVERT: A 11 CYS cc_start: 0.8690 (p) cc_final: 0.8452 (t) REVERT: A 12 LEU cc_start: 0.8894 (mp) cc_final: 0.8499 (tt) REVERT: A 24 MET cc_start: 0.8956 (tpp) cc_final: 0.8237 (mtt) REVERT: A 33 ARG cc_start: 0.8540 (mtt180) cc_final: 0.7641 (ptp90) REVERT: A 43 GLN cc_start: 0.8740 (tp40) cc_final: 0.8307 (tp-100) REVERT: A 60 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 93 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9090 (tp30) REVERT: A 122 TYR cc_start: 0.7954 (m-80) cc_final: 0.7479 (m-80) REVERT: A 123 PHE cc_start: 0.7602 (m-10) cc_final: 0.6342 (t80) REVERT: A 135 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7511 (ttm110) REVERT: A 171 ARG cc_start: 0.8938 (mtm180) cc_final: 0.8305 (ttt180) REVERT: A 245 MET cc_start: 0.8945 (mmm) cc_final: 0.8587 (mmm) REVERT: A 265 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: A 288 ASN cc_start: 0.9070 (t0) cc_final: 0.8763 (m110) REVERT: A 361 MET cc_start: 0.7462 (tmm) cc_final: 0.7118 (tmm) REVERT: A 384 MET cc_start: 0.7974 (tmm) cc_final: 0.7748 (tmm) REVERT: A 388 LEU cc_start: 0.8990 (mt) cc_final: 0.8408 (mp) REVERT: A 631 GLU cc_start: 0.8672 (mp0) cc_final: 0.8214 (pt0) REVERT: A 635 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: A 655 GLU cc_start: 0.7550 (pt0) cc_final: 0.6745 (tm-30) REVERT: A 960 MET cc_start: 0.8711 (ttt) cc_final: 0.7962 (tmm) REVERT: A 969 MET cc_start: 0.8413 (mtp) cc_final: 0.8077 (mtp) REVERT: A 1004 GLN cc_start: 0.8463 (tp40) cc_final: 0.7886 (tp-100) REVERT: A 1040 TYR cc_start: 0.8768 (t80) cc_final: 0.8487 (t80) REVERT: A 1077 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8818 (pm20) REVERT: A 1170 ARG cc_start: 0.8396 (mmt90) cc_final: 0.8028 (mtm180) REVERT: A 1278 MET cc_start: 0.7705 (mtt) cc_final: 0.7245 (ttm) REVERT: A 1334 ASP cc_start: 0.8221 (m-30) cc_final: 0.7730 (t0) REVERT: A 1386 LYS cc_start: 0.9061 (mttm) cc_final: 0.8497 (tppt) REVERT: A 1416 MET cc_start: 0.5352 (ttt) cc_final: 0.4919 (ttm) REVERT: A 1417 MET cc_start: 0.7269 (tmm) cc_final: 0.6686 (tpp) outliers start: 40 outliers final: 31 residues processed: 240 average time/residue: 0.1895 time to fit residues: 64.6502 Evaluate side-chains 241 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1276 ASN Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** A1256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9694 Z= 0.178 Angle : 0.591 8.700 13095 Z= 0.288 Chirality : 0.039 0.177 1503 Planarity : 0.004 0.047 1611 Dihedral : 4.466 37.452 1297 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.57 % Allowed : 24.93 % Favored : 71.50 % 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: 0.00 (0.25), residues: 1174 helix: 0.87 (0.20), residues: 694 sheet: -0.14 (0.72), residues: 48 loop : -1.39 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 887 HIS 0.004 0.001 HIS A1311 PHE 0.030 0.001 PHE A 863 TYR 0.018 0.001 TYR A1342 ARG 0.005 0.000 ARG A 486 *********************** 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 256 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 1.115 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: A 1 MET cc_start: 0.8514 (ppp) cc_final: 0.8107 (ppp) REVERT: A 12 LEU cc_start: 0.8861 (mp) cc_final: 0.8449 (tt) REVERT: A 24 MET cc_start: 0.8949 (tpp) cc_final: 0.8241 (mtt) REVERT: A 33 ARG cc_start: 0.8553 (mtt180) cc_final: 0.7651 (ptp90) REVERT: A 43 GLN cc_start: 0.8695 (tp40) cc_final: 0.8249 (tp-100) REVERT: A 49 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8858 (mm) REVERT: A 60 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8384 (mm-30) REVERT: A 93 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9088 (tp30) REVERT: A 122 TYR cc_start: 0.7951 (m-80) cc_final: 0.7555 (m-80) REVERT: A 123 PHE cc_start: 0.7598 (m-10) cc_final: 0.6381 (t80) REVERT: A 135 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7457 (ttm110) REVERT: A 171 ARG cc_start: 0.8996 (mtm180) cc_final: 0.8385 (ttt180) REVERT: A 245 MET cc_start: 0.8929 (mmm) cc_final: 0.8577 (mmm) REVERT: A 265 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: A 288 ASN cc_start: 0.9074 (t0) cc_final: 0.8766 (m110) REVERT: A 361 MET cc_start: 0.7481 (tmm) cc_final: 0.7111 (tmm) REVERT: A 384 MET cc_start: 0.7951 (tmm) cc_final: 0.7701 (tmm) REVERT: A 388 LEU cc_start: 0.8991 (mt) cc_final: 0.8360 (mp) REVERT: A 631 GLU cc_start: 0.8675 (mp0) cc_final: 0.8461 (pt0) REVERT: A 655 GLU cc_start: 0.7539 (pt0) cc_final: 0.6744 (tm-30) REVERT: A 960 MET cc_start: 0.8705 (ttt) cc_final: 0.7950 (tmm) REVERT: A 994 MET cc_start: 0.7656 (mmm) cc_final: 0.7318 (mtp) REVERT: A 1004 GLN cc_start: 0.8512 (tp40) cc_final: 0.8025 (tp40) REVERT: A 1040 TYR cc_start: 0.8792 (t80) cc_final: 0.8482 (t80) REVERT: A 1077 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8828 (pm20) REVERT: A 1133 LYS cc_start: 0.9264 (pttt) cc_final: 0.8802 (ptmt) REVERT: A 1170 ARG cc_start: 0.8371 (mmt90) cc_final: 0.8010 (mtm180) REVERT: A 1278 MET cc_start: 0.7667 (mtt) cc_final: 0.6374 (ttt) REVERT: A 1334 ASP cc_start: 0.8206 (m-30) cc_final: 0.7722 (t0) REVERT: A 1386 LYS cc_start: 0.9060 (mttm) cc_final: 0.8483 (tppt) REVERT: A 1416 MET cc_start: 0.5380 (ttt) cc_final: 0.4952 (ttm) REVERT: A 1417 MET cc_start: 0.7080 (tmm) cc_final: 0.6448 (tpp) outliers start: 37 outliers final: 28 residues processed: 238 average time/residue: 0.1941 time to fit residues: 65.7832 Evaluate side-chains 243 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0010 chunk 99 optimal weight: 0.0970 chunk 105 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5455 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= 0.155 Angle : 0.594 8.956 13095 Z= 0.285 Chirality : 0.039 0.179 1503 Planarity : 0.004 0.047 1611 Dihedral : 4.453 37.764 1297 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.48 % Allowed : 25.12 % Favored : 71.40 % 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: -0.07 (0.25), residues: 1174 helix: 0.83 (0.20), residues: 701 sheet: -0.05 (0.71), residues: 48 loop : -1.51 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1106 HIS 0.003 0.001 HIS A 666 PHE 0.028 0.001 PHE A 863 TYR 0.017 0.001 TYR A1342 ARG 0.006 0.000 ARG A 486 *********************** 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 253 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8526 (ppp) cc_final: 0.8142 (ppp) REVERT: A 11 CYS cc_start: 0.8672 (p) cc_final: 0.8429 (t) REVERT: A 12 LEU cc_start: 0.8895 (mp) cc_final: 0.8484 (tt) REVERT: A 24 MET cc_start: 0.8915 (tpp) cc_final: 0.8272 (mtt) REVERT: A 33 ARG cc_start: 0.8494 (mtt180) cc_final: 0.7571 (ptp90) REVERT: A 43 GLN cc_start: 0.8718 (tp40) cc_final: 0.8268 (tp-100) REVERT: A 49 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8815 (mm) REVERT: A 60 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 93 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9123 (tp30) REVERT: A 122 TYR cc_start: 0.7882 (m-80) cc_final: 0.7508 (m-80) REVERT: A 123 PHE cc_start: 0.7530 (m-10) cc_final: 0.6322 (t80) REVERT: A 171 ARG cc_start: 0.8981 (mtm180) cc_final: 0.8375 (ttt180) REVERT: A 245 MET cc_start: 0.8910 (mmm) cc_final: 0.8549 (mmm) REVERT: A 265 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: A 288 ASN cc_start: 0.9048 (t0) cc_final: 0.8736 (m110) REVERT: A 361 MET cc_start: 0.7474 (tmm) cc_final: 0.7103 (tmm) REVERT: A 384 MET cc_start: 0.7977 (tmm) cc_final: 0.7707 (tmm) REVERT: A 388 LEU cc_start: 0.8983 (mt) cc_final: 0.8355 (mp) REVERT: A 452 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8088 (tpp) REVERT: A 631 GLU cc_start: 0.8710 (mp0) cc_final: 0.8462 (pt0) REVERT: A 655 GLU cc_start: 0.7523 (pt0) cc_final: 0.6714 (tm-30) REVERT: A 960 MET cc_start: 0.8669 (ttt) cc_final: 0.7930 (tmm) REVERT: A 969 MET cc_start: 0.8418 (mtp) cc_final: 0.8199 (mtp) REVERT: A 994 MET cc_start: 0.7711 (mmm) cc_final: 0.7297 (mtp) REVERT: A 1004 GLN cc_start: 0.8454 (tp40) cc_final: 0.8125 (tp40) REVERT: A 1040 TYR cc_start: 0.8779 (t80) cc_final: 0.8504 (t80) REVERT: A 1077 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8834 (pm20) REVERT: A 1133 LYS cc_start: 0.9245 (pttt) cc_final: 0.8793 (ptmt) REVERT: A 1170 ARG cc_start: 0.8406 (mmt90) cc_final: 0.8012 (mtm180) REVERT: A 1278 MET cc_start: 0.7083 (mtt) cc_final: 0.5839 (ttt) REVERT: A 1334 ASP cc_start: 0.8227 (m-30) cc_final: 0.7746 (t0) REVERT: A 1386 LYS cc_start: 0.9066 (mttm) cc_final: 0.8478 (tppt) REVERT: A 1416 MET cc_start: 0.5292 (ttt) cc_final: 0.4846 (ttm) outliers start: 36 outliers final: 27 residues processed: 237 average time/residue: 0.1951 time to fit residues: 66.1835 Evaluate side-chains 243 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5564 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= 0.161 Angle : 0.614 10.118 13095 Z= 0.293 Chirality : 0.039 0.194 1503 Planarity : 0.004 0.042 1611 Dihedral : 4.477 37.614 1297 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.38 % Allowed : 24.73 % Favored : 71.88 % 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: -0.05 (0.25), residues: 1174 helix: 0.83 (0.20), residues: 704 sheet: 0.09 (0.71), residues: 43 loop : -1.47 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1106 HIS 0.003 0.001 HIS A 666 PHE 0.030 0.001 PHE A 863 TYR 0.016 0.001 TYR A1342 ARG 0.006 0.000 ARG A 486 ********************** 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 254 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8510 (ppp) cc_final: 0.8137 (ppp) REVERT: A 11 CYS cc_start: 0.8663 (p) cc_final: 0.8424 (t) REVERT: A 12 LEU cc_start: 0.8910 (mp) cc_final: 0.8494 (tt) REVERT: A 24 MET cc_start: 0.8918 (tpp) cc_final: 0.8281 (mtt) REVERT: A 33 ARG cc_start: 0.8490 (mtt180) cc_final: 0.7570 (ptp90) REVERT: A 43 GLN cc_start: 0.8723 (tp40) cc_final: 0.8275 (tp-100) REVERT: A 49 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8858 (mm) REVERT: A 60 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 122 TYR cc_start: 0.7903 (m-80) cc_final: 0.7529 (m-80) REVERT: A 123 PHE cc_start: 0.7573 (m-10) cc_final: 0.6358 (t80) REVERT: A 171 ARG cc_start: 0.8998 (mtm180) cc_final: 0.8386 (ttt180) REVERT: A 245 MET cc_start: 0.8906 (mmm) cc_final: 0.8627 (mmm) REVERT: A 265 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7977 (tp30) REVERT: A 267 MET cc_start: 0.8513 (tpp) cc_final: 0.7780 (tmm) REVERT: A 288 ASN cc_start: 0.9046 (t0) cc_final: 0.8724 (m110) REVERT: A 361 MET cc_start: 0.7497 (tmm) cc_final: 0.7122 (tmm) REVERT: A 384 MET cc_start: 0.8010 (tmm) cc_final: 0.7748 (tmm) REVERT: A 388 LEU cc_start: 0.8966 (mt) cc_final: 0.8347 (mp) REVERT: A 452 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8122 (tpp) REVERT: A 554 ARG cc_start: 0.8770 (mmt-90) cc_final: 0.8245 (mmt90) REVERT: A 631 GLU cc_start: 0.8663 (mp0) cc_final: 0.8409 (pt0) REVERT: A 655 GLU cc_start: 0.7575 (pt0) cc_final: 0.6755 (tm-30) REVERT: A 849 ARG cc_start: 0.8649 (mtt180) cc_final: 0.8317 (mmm-85) REVERT: A 969 MET cc_start: 0.8406 (mtp) cc_final: 0.8185 (mtp) REVERT: A 1004 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8164 (tp40) REVERT: A 1040 TYR cc_start: 0.8800 (t80) cc_final: 0.8507 (t80) REVERT: A 1077 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: A 1133 LYS cc_start: 0.9251 (pttt) cc_final: 0.8815 (ptmt) REVERT: A 1170 ARG cc_start: 0.8417 (mmt90) cc_final: 0.8034 (mtm180) REVERT: A 1334 ASP cc_start: 0.8225 (m-30) cc_final: 0.7746 (t0) REVERT: A 1386 LYS cc_start: 0.9048 (mttm) cc_final: 0.8467 (tppt) REVERT: A 1416 MET cc_start: 0.5291 (ttt) cc_final: 0.4850 (ttm) outliers start: 35 outliers final: 30 residues processed: 239 average time/residue: 0.1967 time to fit residues: 66.3034 Evaluate side-chains 248 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1004 GLN Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1276 ASN Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101220 restraints weight = 24645.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104218 restraints weight = 13010.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106277 restraints weight = 8414.641| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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= 0.162 Angle : 0.607 9.155 13095 Z= 0.289 Chirality : 0.039 0.180 1503 Planarity : 0.004 0.052 1611 Dihedral : 4.433 37.570 1297 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.29 % Allowed : 24.93 % Favored : 71.79 % 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: -0.07 (0.24), residues: 1174 helix: 0.81 (0.20), residues: 702 sheet: 0.07 (0.70), residues: 48 loop : -1.48 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1106 HIS 0.003 0.001 HIS A 666 PHE 0.031 0.001 PHE A 136 TYR 0.009 0.001 TYR A1220 ARG 0.006 0.000 ARG A 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2246.49 seconds wall clock time: 41 minutes 0.79 seconds (2460.79 seconds total)