Starting phenix.real_space_refine on Sat Mar 16 02:03:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fuw_4225/03_2024/6fuw_4225_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fuw_4225/03_2024/6fuw_4225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fuw_4225/03_2024/6fuw_4225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fuw_4225/03_2024/6fuw_4225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fuw_4225/03_2024/6fuw_4225_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fuw_4225/03_2024/6fuw_4225_neut.pdb" } resolution = 3.07 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= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 8 5.49 5 S 88 5.16 5 C 8557 2.51 5 N 2337 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 681": "NH1" <-> "NH2" Residue "A ARG 930": "NH1" <-> "NH2" Residue "A PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1065": "NH1" <-> "NH2" Residue "A ARG 1196": "NH1" <-> "NH2" Residue "A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1298": "NH1" <-> "NH2" Residue "A ARG 1299": "NH1" <-> "NH2" Residue "A ARG 1313": "NH1" <-> "NH2" Residue "A PHE 1338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1357": "NH1" <-> "NH2" Residue "A ARG 1379": "NH1" <-> "NH2" Residue "A ARG 1396": "NH1" <-> "NH2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13421 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9367 Classifications: {'peptide': 1181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 61, 'TRANS': 1115} Chain breaks: 13 Chain: "B" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2978 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 897 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 7} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12643 SG CYS C 41 66.982 15.464 93.239 1.00 69.83 S ATOM 12707 SG CYS C 49 70.877 14.348 95.412 1.00 80.63 S ATOM 12742 SG CYS C 55 69.827 17.994 93.870 1.00 71.19 S ATOM 12844 SG CYS C 68 60.014 27.114 109.007 1.00 44.18 S ATOM 12914 SG CYS C 76 63.413 27.947 107.651 1.00 41.47 S ATOM 12959 SG CYS C 82 62.478 24.853 109.583 1.00 54.43 S ATOM 13080 SG CYS C 96 46.707 33.360 118.497 1.00 58.21 S ATOM 13160 SG CYS C 105 44.547 36.326 117.376 1.00 66.76 S ATOM 13198 SG CYS C 110 45.728 34.284 114.951 1.00 62.16 S Time building chain proxies: 7.80, per 1000 atoms: 0.58 Number of scatterers: 13421 At special positions: 0 Unit cell: (107.916, 106.858, 136.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 88 16.00 P 8 15.00 O 2428 8.00 N 2337 7.00 C 8557 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: 5.45 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 49 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 82 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 68 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 96 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 203 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 110 " Number of angles added : 9 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3112 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 28 sheets defined 7.1% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 506 through 509 removed outlier: 3.561A pdb=" N ASN A 509 " --> pdb=" O HIS A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 1352 through 1370 removed outlier: 3.515A pdb=" N ARG A1358 " --> pdb=" O LYS A1354 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1370 " --> pdb=" O LEU A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 removed outlier: 3.752A pdb=" N LEU A1376 " --> pdb=" O HIS A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.834A pdb=" N MET A1383 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1410 Processing helix chain 'A' and resid 1411 through 1423 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.760A pdb=" N THR A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 4.243A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.887A pdb=" N ASN B 104 " --> pdb=" O ASN B 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.853A pdb=" N GLU C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 96 through 101 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 9 removed outlier: 5.869A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.817A pdb=" N PHE A 16 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.674A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 208 removed outlier: 5.800A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TRP A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 244 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL A 254 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 271 removed outlier: 6.574A pdb=" N PHE A 281 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 279 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA A 270 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 277 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN A 290 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG A 313 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.711A pdb=" N VAL A 346 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS A 364 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 373 through 376 removed outlier: 6.233A pdb=" N SER A 391 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER A 468 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 removed outlier: 6.642A pdb=" N GLY A 510 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 11.946A pdb=" N ARG A1019 " --> pdb=" O ASN A1041 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN A1041 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A1037 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A1025 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A1035 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A1027 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A1033 " --> pdb=" O TYR A1027 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.303A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539 removed outlier: 4.063A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 584 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 610 removed outlier: 3.689A pdb=" N VAL A 619 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 627 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 652 removed outlier: 3.844A pdb=" N LYS A 671 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 681 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 695 through 703 removed outlier: 3.703A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 806 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN A 798 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 804 " --> pdb=" O GLN A 798 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.773A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 873 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 931 through 935 removed outlier: 4.193A pdb=" N SER A 941 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 955 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1098 through 1109 removed outlier: 5.190A pdb=" N VAL A1100 " --> pdb=" O CYS A1126 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS A1126 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A1102 " --> pdb=" O GLY A1124 " (cutoff:3.500A) removed outlier: 19.832A pdb=" N LEU A1117 " --> pdb=" O GLU A1146 " (cutoff:3.500A) removed outlier: 15.429A pdb=" N GLU A1146 " --> pdb=" O LEU A1117 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLY A1119 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A1144 " --> pdb=" O GLY A1119 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A1136 " --> pdb=" O LEU A1127 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A1159 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1172 through 1177 removed outlier: 6.766A pdb=" N ALA A1185 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A1175 " --> pdb=" O VAL A1183 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1183 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1204 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER A1194 " --> pdb=" O GLY A1202 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY A1202 " --> pdb=" O SER A1194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1212 through 1218 removed outlier: 6.720A pdb=" N ALA A1225 " --> pdb=" O HIS A1213 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET A1215 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A1223 " --> pdb=" O MET A1215 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER A1217 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A1221 " --> pdb=" O SER A1217 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1255 through 1263 removed outlier: 6.882A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE A1260 " --> pdb=" O GLY A1268 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY A1268 " --> pdb=" O PHE A1260 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL A1262 " --> pdb=" O GLN A1266 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN A1266 " --> pdb=" O VAL A1262 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET A1282 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG A1298 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.801A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.505A pdb=" N ALA B 138 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 143 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 156 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 145 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 166 through 169 removed outlier: 4.084A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 205 through 210 removed outlier: 7.076A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 247 through 251 removed outlier: 3.608A pdb=" N ILE B 270 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AD1, first strand: chain 'B' and resid 334 through 339 removed outlier: 6.579A pdb=" N GLY B 350 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 337 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 348 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP B 339 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 346 " --> pdb=" O TRP B 339 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1083 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: 5.59 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4192 1.33 - 1.45: 2398 1.45 - 1.57: 7017 1.57 - 1.69: 15 1.69 - 1.81: 139 Bond restraints: 13761 Sorted by residual: bond pdb=" CA ARG B 308 " pdb=" C ARG B 308 " ideal model delta sigma weight residual 1.522 1.477 0.044 1.72e-02 3.38e+03 6.61e+00 bond pdb=" CG1 ILE A 585 " pdb=" CD1 ILE A 585 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.12e+00 bond pdb=" CG LEU B 67 " pdb=" CD2 LEU B 67 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" CB ARG A1313 " pdb=" CG ARG A1313 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.55e+00 bond pdb=" CB VAL A 298 " pdb=" CG1 VAL A 298 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.10e+00 ... (remaining 13756 not shown) Histogram of bond angle deviations from ideal: 96.28 - 104.23: 282 104.23 - 112.17: 6910 112.17 - 120.12: 5419 120.12 - 128.07: 5896 128.07 - 136.01: 181 Bond angle restraints: 18688 Sorted by residual: angle pdb=" N VAL A 632 " pdb=" CA VAL A 632 " pdb=" C VAL A 632 " ideal model delta sigma weight residual 113.42 107.91 5.51 1.17e+00 7.31e-01 2.22e+01 angle pdb=" C LYS A 99 " pdb=" N ASP A 100 " pdb=" CA ASP A 100 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C PHE B 210 " pdb=" N SER B 211 " pdb=" CA SER B 211 " ideal model delta sigma weight residual 120.49 126.73 -6.24 1.42e+00 4.96e-01 1.93e+01 angle pdb=" C GLY B 329 " pdb=" N HIS B 330 " pdb=" CA HIS B 330 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CA LEU B 356 " pdb=" CB LEU B 356 " pdb=" CG LEU B 356 " ideal model delta sigma weight residual 116.30 127.67 -11.37 3.50e+00 8.16e-02 1.05e+01 ... (remaining 18683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 8020 23.94 - 47.87: 144 47.87 - 71.81: 16 71.81 - 95.74: 8 95.74 - 119.68: 1 Dihedral angle restraints: 8189 sinusoidal: 3375 harmonic: 4814 Sorted by residual: dihedral pdb=" CA GLY B 183 " pdb=" C GLY B 183 " pdb=" N TYR B 184 " pdb=" CA TYR B 184 " ideal model delta harmonic sigma weight residual 180.00 -150.52 -29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" O4' A D 1 " pdb=" C1' A D 1 " pdb=" N9 A D 1 " pdb=" C4 A D 1 " ideal model delta sinusoidal sigma weight residual 254.00 166.31 87.69 1 1.70e+01 3.46e-03 3.19e+01 dihedral pdb=" CA SER A1290 " pdb=" C SER A1290 " pdb=" N PHE A1291 " pdb=" CA PHE A1291 " ideal model delta harmonic sigma weight residual 180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 8186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1111 0.041 - 0.082: 627 0.082 - 0.123: 277 0.123 - 0.164: 54 0.164 - 0.205: 12 Chirality restraints: 2081 Sorted by residual: chirality pdb=" CG LEU A 393 " pdb=" CB LEU A 393 " pdb=" CD1 LEU A 393 " pdb=" CD2 LEU A 393 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR B 155 " pdb=" CA THR B 155 " pdb=" OG1 THR B 155 " pdb=" CG2 THR B 155 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A1141 " pdb=" N ILE A1141 " pdb=" C ILE A1141 " pdb=" CB ILE A1141 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2078 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1074 " -0.015 2.00e-02 2.50e+03 2.30e-02 9.29e+00 pdb=" CG PHE A1074 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A1074 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A1074 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A1074 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A1074 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A1074 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 252 " -0.025 2.00e-02 2.50e+03 1.82e-02 8.30e+00 pdb=" CG TRP B 252 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 252 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 252 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 252 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 252 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 252 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 252 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 252 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 345 " -0.018 2.00e-02 2.50e+03 1.93e-02 7.47e+00 pdb=" CG TYR A 345 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 345 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 345 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 345 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 345 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 345 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 345 " 0.000 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1394 2.73 - 3.28: 12019 3.28 - 3.82: 20596 3.82 - 4.36: 26475 4.36 - 4.90: 47067 Nonbonded interactions: 107551 Sorted by model distance: nonbonded pdb=" OD1 ASP A 130 " pdb=" NH2 ARG A 158 " model vdw 2.193 2.520 nonbonded pdb=" O TYR A 19 " pdb=" NH2 ARG A 28 " model vdw 2.198 2.520 nonbonded pdb=" OD1 ASP A1263 " pdb=" N ASN A1264 " model vdw 2.214 2.520 nonbonded pdb=" NE2 GLN B 325 " pdb=" O VAL B 361 " model vdw 2.217 2.520 nonbonded pdb=" OG SER B 162 " pdb=" O HIS B 181 " model vdw 2.218 2.440 ... (remaining 107546 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.600 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 42.750 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.010 0.079 13761 Z= 0.673 Angle : 0.982 15.305 18688 Z= 0.518 Chirality : 0.058 0.205 2081 Planarity : 0.006 0.065 2352 Dihedral : 10.532 119.677 5077 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.10 (0.17), residues: 1631 helix: -2.78 (0.43), residues: 78 sheet: -2.00 (0.19), residues: 581 loop : -3.33 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP B 252 HIS 0.015 0.003 HIS A 979 PHE 0.051 0.004 PHE A1074 TYR 0.046 0.004 TYR A 345 ARG 0.015 0.002 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.8894 (ttp) cc_final: 0.8558 (ttm) REVERT: A 213 TYR cc_start: 0.5555 (t80) cc_final: 0.5284 (t80) REVERT: A 328 THR cc_start: 0.8650 (p) cc_final: 0.8387 (t) REVERT: A 580 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6086 (mm-30) REVERT: A 612 ILE cc_start: 0.8030 (mt) cc_final: 0.7775 (mm) REVERT: A 614 ASP cc_start: 0.7915 (m-30) cc_final: 0.7684 (t0) REVERT: A 628 LEU cc_start: 0.7738 (pp) cc_final: 0.7304 (tt) REVERT: A 662 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7162 (mm-30) REVERT: A 809 LYS cc_start: 0.7379 (mtpp) cc_final: 0.7153 (mmtm) REVERT: C 19 VAL cc_start: 0.6658 (t) cc_final: 0.6444 (m) REVERT: C 27 PRO cc_start: 0.8155 (Cg_exo) cc_final: 0.7950 (Cg_endo) REVERT: C 46 LYS cc_start: 0.7705 (mmpt) cc_final: 0.6671 (ptpt) REVERT: C 77 LYS cc_start: 0.8190 (mttp) cc_final: 0.7626 (pttm) REVERT: C 87 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7592 (mt-10) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3312 time to fit residues: 132.9005 Evaluate side-chains 159 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 315 GLN A 620 GLN A1220 ASN A1307 HIS A1373 HIS B 53 ASN B 60 ASN B 69 ASN B 330 HIS B 405 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13761 Z= 0.160 Angle : 0.602 12.004 18688 Z= 0.311 Chirality : 0.045 0.168 2081 Planarity : 0.004 0.053 2352 Dihedral : 8.088 109.163 1908 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.24 % Allowed : 6.49 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.12 (0.18), residues: 1631 helix: -1.38 (0.50), residues: 89 sheet: -1.33 (0.20), residues: 591 loop : -2.74 (0.17), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 952 HIS 0.004 0.001 HIS A 113 PHE 0.017 0.001 PHE A 600 TYR 0.012 0.001 TYR C 99 ARG 0.003 0.000 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7097 (mtm-85) REVERT: A 213 TYR cc_start: 0.5366 (t80) cc_final: 0.5144 (t80) REVERT: A 260 SER cc_start: 0.7040 (m) cc_final: 0.6820 (p) REVERT: A 328 THR cc_start: 0.8617 (p) cc_final: 0.8340 (t) REVERT: A 580 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6313 (mm-30) REVERT: A 614 ASP cc_start: 0.7861 (m-30) cc_final: 0.7611 (t0) REVERT: A 662 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6918 (mm-30) REVERT: A 937 ILE cc_start: 0.8032 (tt) cc_final: 0.7702 (tt) REVERT: A 1220 ASN cc_start: 0.6884 (t0) cc_final: 0.6671 (t0) REVERT: B 49 ARG cc_start: 0.7235 (ppt90) cc_final: 0.6891 (ppt170) REVERT: C 1 MET cc_start: 0.5196 (ptm) cc_final: 0.4603 (ptm) REVERT: C 19 VAL cc_start: 0.6871 (t) cc_final: 0.6578 (m) REVERT: C 46 LYS cc_start: 0.7553 (mmpt) cc_final: 0.6393 (ptpt) REVERT: C 77 LYS cc_start: 0.7996 (mttp) cc_final: 0.7571 (pttm) REVERT: C 87 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7499 (mt-10) outliers start: 18 outliers final: 11 residues processed: 218 average time/residue: 0.2950 time to fit residues: 90.2601 Evaluate side-chains 170 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 163 optimal weight: 0.0000 chunk 134 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 2.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 252 HIS A 798 GLN A 993 GLN A1237 GLN A1352 GLN B 189 GLN B 310 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13761 Z= 0.284 Angle : 0.636 12.613 18688 Z= 0.326 Chirality : 0.046 0.181 2081 Planarity : 0.005 0.056 2352 Dihedral : 8.078 108.698 1908 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.11 % Allowed : 7.80 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.67 (0.19), residues: 1631 helix: -0.83 (0.54), residues: 83 sheet: -0.96 (0.21), residues: 590 loop : -2.51 (0.17), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 252 HIS 0.008 0.001 HIS A 979 PHE 0.016 0.002 PHE A 600 TYR 0.018 0.002 TYR A 345 ARG 0.003 0.001 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7132 (mtm-85) REVERT: A 166 ARG cc_start: 0.7352 (mmm-85) cc_final: 0.6740 (mmp80) REVERT: A 213 TYR cc_start: 0.5555 (t80) cc_final: 0.5264 (t80) REVERT: A 260 SER cc_start: 0.7183 (m) cc_final: 0.6913 (p) REVERT: A 328 THR cc_start: 0.8639 (p) cc_final: 0.8381 (t) REVERT: A 580 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6303 (mm-30) REVERT: A 614 ASP cc_start: 0.7908 (m-30) cc_final: 0.7655 (t0) REVERT: A 630 GLU cc_start: 0.6509 (tt0) cc_final: 0.6004 (tm-30) REVERT: A 642 LEU cc_start: 0.4364 (OUTLIER) cc_final: 0.3666 (pp) REVERT: A 662 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6907 (mm-30) REVERT: A 901 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7695 (m-10) REVERT: A 937 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7629 (tt) REVERT: A 1207 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: A 1432 ASP cc_start: 0.6650 (m-30) cc_final: 0.6316 (m-30) REVERT: B 49 ARG cc_start: 0.7264 (ppt90) cc_final: 0.6925 (ppt170) REVERT: B 198 PHE cc_start: 0.4523 (t80) cc_final: 0.4003 (t80) REVERT: C 1 MET cc_start: 0.5326 (ptm) cc_final: 0.4615 (ptm) REVERT: C 19 VAL cc_start: 0.7157 (t) cc_final: 0.6805 (m) REVERT: C 46 LYS cc_start: 0.7623 (mmpt) cc_final: 0.6462 (ptpt) REVERT: C 77 LYS cc_start: 0.8205 (mttp) cc_final: 0.7635 (pttm) REVERT: C 87 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7440 (mt-10) REVERT: C 90 MET cc_start: 0.7354 (mmp) cc_final: 0.6894 (mmp) outliers start: 45 outliers final: 27 residues processed: 205 average time/residue: 0.2746 time to fit residues: 80.7710 Evaluate side-chains 195 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS A1220 ASN A1307 HIS B 73 GLN B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13761 Z= 0.320 Angle : 0.648 13.083 18688 Z= 0.331 Chirality : 0.046 0.161 2081 Planarity : 0.005 0.059 2352 Dihedral : 8.099 109.040 1908 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.17 % Allowed : 9.32 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.50 (0.19), residues: 1631 helix: -0.90 (0.55), residues: 84 sheet: -0.76 (0.21), residues: 597 loop : -2.44 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 252 HIS 0.008 0.002 HIS A 979 PHE 0.017 0.002 PHE A 708 TYR 0.013 0.002 TYR A 345 ARG 0.003 0.001 ARG A1235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 1.676 Fit side-chains REVERT: A 45 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.7137 (mtm-85) REVERT: A 166 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6786 (mpt180) REVERT: A 260 SER cc_start: 0.7193 (m) cc_final: 0.6935 (p) REVERT: A 328 THR cc_start: 0.8726 (p) cc_final: 0.8442 (t) REVERT: A 593 MET cc_start: 0.7619 (tpt) cc_final: 0.7197 (mmt) REVERT: A 630 GLU cc_start: 0.6349 (tt0) cc_final: 0.5783 (tm-30) REVERT: A 642 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.3657 (pp) REVERT: A 662 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6899 (mm-30) REVERT: A 901 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: A 937 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7662 (tt) REVERT: A 1056 GLU cc_start: 0.7488 (mp0) cc_final: 0.6878 (pt0) REVERT: A 1207 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: A 1432 ASP cc_start: 0.6660 (m-30) cc_final: 0.6324 (m-30) REVERT: B 49 ARG cc_start: 0.7349 (ppt90) cc_final: 0.7024 (ppt170) REVERT: B 198 PHE cc_start: 0.4612 (t80) cc_final: 0.3907 (t80) REVERT: C 1 MET cc_start: 0.5259 (ptm) cc_final: 0.4538 (ptm) REVERT: C 19 VAL cc_start: 0.7246 (t) cc_final: 0.6959 (m) REVERT: C 46 LYS cc_start: 0.7643 (mmpt) cc_final: 0.6513 (ptpt) REVERT: C 77 LYS cc_start: 0.8147 (mttp) cc_final: 0.7598 (pttm) REVERT: C 87 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7447 (mt-10) REVERT: C 90 MET cc_start: 0.7276 (mmp) cc_final: 0.6787 (mmp) outliers start: 46 outliers final: 33 residues processed: 199 average time/residue: 0.2986 time to fit residues: 85.6013 Evaluate side-chains 192 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 81 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1077 GLN A1220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13761 Z= 0.170 Angle : 0.550 11.285 18688 Z= 0.284 Chirality : 0.043 0.163 2081 Planarity : 0.004 0.060 2352 Dihedral : 7.704 104.014 1908 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.69 % Allowed : 10.21 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.14 (0.20), residues: 1631 helix: -0.52 (0.57), residues: 85 sheet: -0.55 (0.21), residues: 620 loop : -2.22 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 952 HIS 0.004 0.001 HIS A 113 PHE 0.011 0.001 PHE A 877 TYR 0.014 0.001 TYR C 99 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.604 Fit side-chains REVERT: A 45 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7199 (mtm-85) REVERT: A 166 ARG cc_start: 0.7376 (mmm-85) cc_final: 0.6973 (mpt180) REVERT: A 220 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8269 (tp) REVERT: A 260 SER cc_start: 0.7069 (m) cc_final: 0.6831 (p) REVERT: A 328 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8466 (t) REVERT: A 593 MET cc_start: 0.7554 (tpt) cc_final: 0.7143 (mmt) REVERT: A 630 GLU cc_start: 0.6504 (tt0) cc_final: 0.5946 (tm-30) REVERT: A 662 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6896 (mm-30) REVERT: A 901 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: A 1056 GLU cc_start: 0.7479 (mp0) cc_final: 0.6821 (pt0) REVERT: A 1220 ASN cc_start: 0.7170 (t0) cc_final: 0.6879 (t0) REVERT: A 1432 ASP cc_start: 0.6599 (m-30) cc_final: 0.6324 (m-30) REVERT: B 49 ARG cc_start: 0.7192 (ppt90) cc_final: 0.6930 (ppt170) REVERT: B 98 MET cc_start: 0.8298 (ptt) cc_final: 0.8042 (ptm) REVERT: B 198 PHE cc_start: 0.4680 (t80) cc_final: 0.3888 (t80) REVERT: C 1 MET cc_start: 0.5144 (ptm) cc_final: 0.4431 (ptm) REVERT: C 19 VAL cc_start: 0.7429 (t) cc_final: 0.7151 (m) REVERT: C 46 LYS cc_start: 0.7625 (mmpt) cc_final: 0.6495 (ptpt) REVERT: C 77 LYS cc_start: 0.8101 (mttp) cc_final: 0.7588 (pttm) REVERT: C 87 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7415 (mt-10) REVERT: C 90 MET cc_start: 0.7198 (mmp) cc_final: 0.6578 (mmp) outliers start: 39 outliers final: 26 residues processed: 205 average time/residue: 0.2862 time to fit residues: 83.9237 Evaluate side-chains 193 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1077 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13761 Z= 0.283 Angle : 0.616 12.337 18688 Z= 0.315 Chirality : 0.045 0.186 2081 Planarity : 0.004 0.063 2352 Dihedral : 7.859 103.861 1908 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.04 % Allowed : 10.49 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.14 (0.20), residues: 1631 helix: -0.64 (0.55), residues: 85 sheet: -0.53 (0.21), residues: 617 loop : -2.21 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 252 HIS 0.007 0.001 HIS A 979 PHE 0.014 0.002 PHE A 978 TYR 0.016 0.002 TYR C 99 ARG 0.003 0.000 ARG A1235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7137 (mtm-85) REVERT: A 166 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.6971 (mpt180) REVERT: A 205 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7414 (t70) REVERT: A 260 SER cc_start: 0.7008 (m) cc_final: 0.6743 (p) REVERT: A 328 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8484 (t) REVERT: A 592 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7106 (mm) REVERT: A 593 MET cc_start: 0.7616 (tpt) cc_final: 0.7185 (mmt) REVERT: A 630 GLU cc_start: 0.6331 (tt0) cc_final: 0.5868 (tm-30) REVERT: A 642 LEU cc_start: 0.4330 (OUTLIER) cc_final: 0.3718 (pp) REVERT: A 662 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6906 (mm-30) REVERT: A 901 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7687 (m-10) REVERT: A 937 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 1056 GLU cc_start: 0.7511 (mp0) cc_final: 0.6906 (pt0) REVERT: A 1207 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: A 1432 ASP cc_start: 0.6660 (m-30) cc_final: 0.6377 (m-30) REVERT: B 49 ARG cc_start: 0.7200 (ppt90) cc_final: 0.6939 (ppt170) REVERT: C 19 VAL cc_start: 0.7523 (t) cc_final: 0.7211 (m) REVERT: C 46 LYS cc_start: 0.7684 (mmpt) cc_final: 0.6679 (ptpt) REVERT: C 77 LYS cc_start: 0.8139 (mttp) cc_final: 0.7594 (pttm) REVERT: C 87 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 90 MET cc_start: 0.7260 (mmp) cc_final: 0.6816 (mmp) REVERT: C 102 PHE cc_start: 0.6344 (m-80) cc_final: 0.6052 (m-80) outliers start: 44 outliers final: 34 residues processed: 193 average time/residue: 0.2776 time to fit residues: 76.9622 Evaluate side-chains 197 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 100 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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: 0.7834 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13761 Z= 0.148 Angle : 0.529 10.349 18688 Z= 0.274 Chirality : 0.043 0.189 2081 Planarity : 0.004 0.061 2352 Dihedral : 7.441 99.000 1908 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.42 % Allowed : 11.39 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.80 (0.20), residues: 1631 helix: -0.07 (0.58), residues: 84 sheet: -0.32 (0.21), residues: 618 loop : -2.00 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE A 877 TYR 0.014 0.001 TYR C 99 ARG 0.004 0.000 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7188 (mtm-85) REVERT: A 166 ARG cc_start: 0.7225 (mmm-85) cc_final: 0.7020 (mpt180) REVERT: A 260 SER cc_start: 0.6902 (m) cc_final: 0.6671 (p) REVERT: A 328 THR cc_start: 0.8778 (p) cc_final: 0.8544 (t) REVERT: A 593 MET cc_start: 0.7477 (tpt) cc_final: 0.7096 (mmt) REVERT: A 630 GLU cc_start: 0.6490 (tt0) cc_final: 0.6029 (tm-30) REVERT: A 642 LEU cc_start: 0.4483 (OUTLIER) cc_final: 0.3802 (mt) REVERT: A 662 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6882 (mm-30) REVERT: A 1056 GLU cc_start: 0.7440 (mp0) cc_final: 0.6878 (pt0) REVERT: A 1131 GLU cc_start: 0.6867 (mp0) cc_final: 0.6454 (pm20) REVERT: A 1432 ASP cc_start: 0.6555 (m-30) cc_final: 0.6312 (m-30) REVERT: B 49 ARG cc_start: 0.7074 (ppt90) cc_final: 0.6852 (ppt170) REVERT: B 98 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8085 (ptm) REVERT: C 1 MET cc_start: 0.5090 (ptm) cc_final: 0.4414 (ptm) REVERT: C 19 VAL cc_start: 0.7494 (t) cc_final: 0.7219 (m) REVERT: C 77 LYS cc_start: 0.8093 (mttp) cc_final: 0.7567 (pttm) REVERT: C 87 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 90 MET cc_start: 0.7159 (mmp) cc_final: 0.6648 (mmp) REVERT: C 102 PHE cc_start: 0.6517 (m-80) cc_final: 0.6310 (m-80) outliers start: 35 outliers final: 23 residues processed: 192 average time/residue: 0.2667 time to fit residues: 74.2449 Evaluate side-chains 183 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 145 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 879 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13761 Z= 0.210 Angle : 0.564 11.132 18688 Z= 0.290 Chirality : 0.044 0.190 2081 Planarity : 0.004 0.061 2352 Dihedral : 7.468 95.997 1908 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.55 % Allowed : 11.87 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.75 (0.20), residues: 1631 helix: -0.12 (0.57), residues: 84 sheet: -0.25 (0.21), residues: 616 loop : -1.98 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 359 HIS 0.005 0.001 HIS A 979 PHE 0.011 0.001 PHE A 527 TYR 0.015 0.001 TYR C 99 ARG 0.004 0.000 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.7168 (mtm-85) REVERT: A 166 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6859 (tpp-160) REVERT: A 260 SER cc_start: 0.7046 (m) cc_final: 0.6802 (p) REVERT: A 328 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (t) REVERT: A 630 GLU cc_start: 0.6388 (tt0) cc_final: 0.5958 (tm-30) REVERT: A 642 LEU cc_start: 0.4496 (OUTLIER) cc_final: 0.3689 (mt) REVERT: A 662 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6911 (mm-30) REVERT: A 901 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: A 1056 GLU cc_start: 0.7509 (mp0) cc_final: 0.6874 (pt0) REVERT: A 1131 GLU cc_start: 0.6915 (mp0) cc_final: 0.6494 (pm20) REVERT: A 1432 ASP cc_start: 0.6590 (m-30) cc_final: 0.6348 (m-30) REVERT: B 98 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8090 (ptm) REVERT: C 1 MET cc_start: 0.5124 (ptm) cc_final: 0.4433 (ptm) REVERT: C 19 VAL cc_start: 0.7529 (t) cc_final: 0.7235 (m) REVERT: C 77 LYS cc_start: 0.8154 (mttp) cc_final: 0.7557 (pttm) REVERT: C 87 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 90 MET cc_start: 0.7207 (mmp) cc_final: 0.6760 (mmp) outliers start: 37 outliers final: 31 residues processed: 181 average time/residue: 0.2708 time to fit residues: 71.0807 Evaluate side-chains 184 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 89 optimal weight: 0.0060 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A1220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13761 Z= 0.129 Angle : 0.512 9.771 18688 Z= 0.264 Chirality : 0.043 0.187 2081 Planarity : 0.004 0.059 2352 Dihedral : 7.159 91.584 1908 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.93 % Allowed : 13.04 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.53 (0.20), residues: 1631 helix: 0.27 (0.59), residues: 83 sheet: -0.08 (0.21), residues: 618 loop : -1.87 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 229 HIS 0.003 0.000 HIS A 113 PHE 0.009 0.001 PHE A 877 TYR 0.014 0.001 TYR C 99 ARG 0.004 0.000 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7212 (mtm-85) REVERT: A 166 ARG cc_start: 0.7252 (mmm-85) cc_final: 0.7052 (mpt180) REVERT: A 260 SER cc_start: 0.6878 (m) cc_final: 0.6650 (p) REVERT: A 630 GLU cc_start: 0.6404 (tt0) cc_final: 0.5973 (tm-30) REVERT: A 642 LEU cc_start: 0.4226 (OUTLIER) cc_final: 0.3538 (mt) REVERT: A 901 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: A 1056 GLU cc_start: 0.7500 (mp0) cc_final: 0.6897 (pt0) REVERT: A 1131 GLU cc_start: 0.6888 (mp0) cc_final: 0.6625 (pm20) REVERT: A 1432 ASP cc_start: 0.6531 (m-30) cc_final: 0.6303 (m-30) REVERT: B 98 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8094 (ptm) REVERT: B 256 LYS cc_start: 0.7439 (mttt) cc_final: 0.7176 (mtpt) REVERT: C 1 MET cc_start: 0.5136 (ptm) cc_final: 0.4464 (ptm) REVERT: C 19 VAL cc_start: 0.7413 (t) cc_final: 0.7152 (m) REVERT: C 58 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7355 (mtp180) REVERT: C 77 LYS cc_start: 0.8086 (mttp) cc_final: 0.7453 (pttm) REVERT: C 87 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 90 MET cc_start: 0.7139 (mmp) cc_final: 0.6629 (mmp) outliers start: 28 outliers final: 19 residues processed: 187 average time/residue: 0.2787 time to fit residues: 74.8313 Evaluate side-chains 181 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.0870 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13761 Z= 0.227 Angle : 0.579 10.876 18688 Z= 0.296 Chirality : 0.044 0.185 2081 Planarity : 0.004 0.058 2352 Dihedral : 7.291 86.667 1908 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.93 % Allowed : 13.39 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.20), residues: 1631 helix: 0.18 (0.58), residues: 83 sheet: -0.13 (0.21), residues: 623 loop : -1.89 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 252 HIS 0.005 0.001 HIS A 979 PHE 0.011 0.001 PHE A 978 TYR 0.015 0.001 TYR C 99 ARG 0.003 0.000 ARG A 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.860 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7217 (mtm-85) REVERT: A 166 ARG cc_start: 0.7229 (mmm-85) cc_final: 0.6865 (tpp-160) REVERT: A 260 SER cc_start: 0.7023 (m) cc_final: 0.6777 (p) REVERT: A 630 GLU cc_start: 0.6428 (tt0) cc_final: 0.6028 (tm-30) REVERT: A 642 LEU cc_start: 0.4585 (OUTLIER) cc_final: 0.3687 (mt) REVERT: A 901 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7704 (m-10) REVERT: A 1056 GLU cc_start: 0.7485 (mp0) cc_final: 0.6882 (pt0) REVERT: A 1131 GLU cc_start: 0.6945 (mp0) cc_final: 0.6565 (pm20) REVERT: A 1432 ASP cc_start: 0.6608 (m-30) cc_final: 0.6380 (m-30) REVERT: B 98 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (ptm) REVERT: C 1 MET cc_start: 0.5136 (ptm) cc_final: 0.4445 (ptm) REVERT: C 19 VAL cc_start: 0.7498 (t) cc_final: 0.7209 (m) REVERT: C 58 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7371 (mtp180) REVERT: C 77 LYS cc_start: 0.8170 (mttp) cc_final: 0.7517 (pttm) REVERT: C 87 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 90 MET cc_start: 0.7204 (mmp) cc_final: 0.6740 (mmp) outliers start: 28 outliers final: 25 residues processed: 175 average time/residue: 0.2802 time to fit residues: 70.5329 Evaluate side-chains 180 residues out of total 1449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132727 restraints weight = 17102.331| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.58 r_work: 0.3506 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13761 Z= 0.155 Angle : 0.546 10.018 18688 Z= 0.278 Chirality : 0.043 0.202 2081 Planarity : 0.004 0.057 2352 Dihedral : 7.122 84.398 1908 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.07 % Allowed : 13.46 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.41 (0.20), residues: 1631 helix: 0.51 (0.60), residues: 83 sheet: 0.01 (0.21), residues: 618 loop : -1.81 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 229 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE A 877 TYR 0.015 0.001 TYR C 99 ARG 0.004 0.000 ARG B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3066.97 seconds wall clock time: 57 minutes 35.60 seconds (3455.60 seconds total)