Starting phenix.real_space_refine on Wed Feb 14 04:14:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/02_2024/7jlu_22380.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/02_2024/7jlu_22380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/02_2024/7jlu_22380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/02_2024/7jlu_22380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/02_2024/7jlu_22380.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlu_22380/02_2024/7jlu_22380.pdb" } resolution = 3.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 52 5.16 5 C 5499 2.51 5 N 1460 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 657": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A ASP 699": "OD1" <-> "OD2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A ASP 841": "OD1" <-> "OD2" Residue "A ASP 885": "OD1" <-> "OD2" Residue "A PHE 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A GLU 931": "OE1" <-> "OE2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A PHE 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1025": "OE1" <-> "OE2" Residue "A TYR 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1049": "OE1" <-> "OE2" Residue "A ASP 1050": "OD1" <-> "OD2" Residue "A TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A GLU 1087": "OE1" <-> "OE2" Residue "A ASP 1096": "OD1" <-> "OD2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1113": "OE1" <-> "OE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1170": "OD1" <-> "OD2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1199": "OE1" <-> "OE2" Residue "A ASP 1201": "OD1" <-> "OD2" Residue "A GLU 1204": "OE1" <-> "OE2" Residue "A PHE 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1234": "NH1" <-> "NH2" Residue "A PHE 1243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1278": "NH1" <-> "NH2" Residue "A PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1292": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 399": "OD1" <-> "OD2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B GLU 440": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8592 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5884 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 31, 'TRANS': 694} Chain breaks: 3 Chain: "B" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2708 Unusual residues: {' CA': 1} Classifications: {'peptide': 353, 'undetermined': 1} Link IDs: {'PTRANS': 24, 'TRANS': 328, None: 1} Not linked: pdbres="ALA B 453 " pdbres=" CA B 501 " Chain breaks: 1 Time building chain proxies: 5.26, per 1000 atoms: 0.61 Number of scatterers: 8592 At special positions: 0 Unit cell: (96.6758, 108.878, 94.7986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 52 16.00 O 1580 8.00 N 1460 7.00 C 5499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 31.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.885A pdb=" N TYR A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.549A pdb=" N LEU A 669 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.853A pdb=" N ILE A 736 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU A 737 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 763 Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.638A pdb=" N ASN A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 831 removed outlier: 3.658A pdb=" N GLY A 830 " --> pdb=" O SER A 827 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 831 " --> pdb=" O ILE A 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 827 through 831' Processing helix chain 'A' and resid 896 through 901 removed outlier: 3.827A pdb=" N ILE A 899 " --> pdb=" O PRO A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 949 removed outlier: 3.520A pdb=" N LEU A 949 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 976 removed outlier: 3.855A pdb=" N LEU A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 1044 through 1052 removed outlier: 3.590A pdb=" N MET A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 4.007A pdb=" N TYR A1072 " --> pdb=" O TYR A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1079 removed outlier: 3.570A pdb=" N ILE A1078 " --> pdb=" O LEU A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1100 removed outlier: 4.271A pdb=" N GLU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN A1092 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN A1093 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 4.141A pdb=" N THR A1148 " --> pdb=" O TYR A1145 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A1149 " --> pdb=" O TRP A1146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1145 through 1149' Processing helix chain 'A' and resid 1166 through 1178 removed outlier: 3.629A pdb=" N ASP A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1190 removed outlier: 3.716A pdb=" N GLU A1189 " --> pdb=" O TYR A1186 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A1190 " --> pdb=" O TRP A1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 121 through 136 removed outlier: 3.706A pdb=" N VAL B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 168 Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.517A pdb=" N GLY B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 removed outlier: 3.570A pdb=" N GLU B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 245 through 252 Processing helix chain 'B' and resid 278 through 284 removed outlier: 4.160A pdb=" N ASP B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.600A pdb=" N GLU B 321 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 350 removed outlier: 3.656A pdb=" N GLN B 350 " --> pdb=" O TRP B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 407 removed outlier: 3.911A pdb=" N THR B 402 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 415 removed outlier: 3.895A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.625A pdb=" N LEU A 529 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 561 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 531 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 560 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 605 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER A 631 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET A 607 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.805A pdb=" N ILE A 690 " --> pdb=" O GLU A 711 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 744 through 748 removed outlier: 7.046A pdb=" N VAL A 795 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 790 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N CYS A 816 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 792 " --> pdb=" O CYS A 816 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 813 " --> pdb=" O LYS A 838 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU A 840 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 815 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE A 884 " --> pdb=" O CYS A 909 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER A 911 " --> pdb=" O ILE A 884 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET A 886 " --> pdb=" O SER A 911 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A1040 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS A1120 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1238 " --> pdb=" O PHE A1162 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A1162 " --> pdb=" O VAL A1238 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A1246 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A1154 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY A1153 " --> pdb=" O VAL A1289 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A1289 " --> pdb=" O GLY A1153 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A1155 " --> pdb=" O ASN A1287 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A1287 " --> pdb=" O ALA A1155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1140 removed outlier: 3.590A pdb=" N CYS A1271 " --> pdb=" O THR A1206 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A1223 " --> pdb=" O ALA A1207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 174 through 176 removed outlier: 5.398A pdb=" N LEU B 109 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 141 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 111 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 143 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP B 110 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL B 230 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 112 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 227 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 256 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE B 258 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 231 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ARG B 303 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 256 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B 305 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 258 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 302 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 431 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 304 " --> pdb=" O VAL B 431 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 699 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: 3.12 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2793 1.34 - 1.46: 1911 1.46 - 1.58: 3998 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8780 Sorted by residual: bond pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.20e+00 bond pdb=" CA THR B 147 " pdb=" C THR B 147 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.24e-02 6.50e+03 8.96e-01 bond pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.43e-01 bond pdb=" CA ASN A 744 " pdb=" CB ASN A 744 " ideal model delta sigma weight residual 1.535 1.554 -0.019 2.09e-02 2.29e+03 8.33e-01 bond pdb=" CB ASP B 150 " pdb=" CG ASP B 150 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.91e-01 ... (remaining 8775 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.90: 296 106.90 - 113.69: 4788 113.69 - 120.48: 3452 120.48 - 127.27: 3261 127.27 - 134.06: 108 Bond angle restraints: 11905 Sorted by residual: angle pdb=" CA LEU B 334 " pdb=" CB LEU B 334 " pdb=" CG LEU B 334 " ideal model delta sigma weight residual 116.30 127.79 -11.49 3.50e+00 8.16e-02 1.08e+01 angle pdb=" CA GLU B 251 " pdb=" CB GLU B 251 " pdb=" CG GLU B 251 " ideal model delta sigma weight residual 114.10 120.41 -6.31 2.00e+00 2.50e-01 9.95e+00 angle pdb=" CB MET A1241 " pdb=" CG MET A1241 " pdb=" SD MET A1241 " ideal model delta sigma weight residual 112.70 120.82 -8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" CB MET B 383 " pdb=" CG MET B 383 " pdb=" SD MET B 383 " ideal model delta sigma weight residual 112.70 120.76 -8.06 3.00e+00 1.11e-01 7.22e+00 angle pdb=" C ALA B 351 " pdb=" N ASN B 352 " pdb=" CA ASN B 352 " ideal model delta sigma weight residual 121.54 126.63 -5.09 1.91e+00 2.74e-01 7.09e+00 ... (remaining 11900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4548 17.96 - 35.92: 634 35.92 - 53.89: 117 53.89 - 71.85: 18 71.85 - 89.81: 7 Dihedral angle restraints: 5324 sinusoidal: 2162 harmonic: 3162 Sorted by residual: dihedral pdb=" CA SER A 590 " pdb=" C SER A 590 " pdb=" N ASN A 591 " pdb=" CA ASN A 591 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA TRP A 900 " pdb=" C TRP A 900 " pdb=" N MET A 901 " pdb=" CA MET A 901 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ARG A1133 " pdb=" C ARG A1133 " pdb=" N SER A1134 " pdb=" CA SER A1134 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 777 0.033 - 0.066: 367 0.066 - 0.099: 137 0.099 - 0.131: 60 0.131 - 0.164: 9 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA GLU A 743 " pdb=" N GLU A 743 " pdb=" C GLU A 743 " pdb=" CB GLU A 743 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CG LEU A 630 " pdb=" CB LEU A 630 " pdb=" CD1 LEU A 630 " pdb=" CD2 LEU A 630 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CB THR A1299 " pdb=" CA THR A1299 " pdb=" OG1 THR A1299 " pdb=" CG2 THR A1299 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1347 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 900 " 0.017 2.00e-02 2.50e+03 1.46e-02 5.32e+00 pdb=" CG TRP A 900 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 900 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 900 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 900 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 900 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 900 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 900 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 900 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 900 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 800 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 801 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 801 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 801 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 385 " -0.006 2.00e-02 2.50e+03 1.22e-02 2.59e+00 pdb=" CG PHE B 385 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE B 385 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 385 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 385 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 385 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 385 " -0.000 2.00e-02 2.50e+03 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 475 2.73 - 3.27: 8625 3.27 - 3.81: 13132 3.81 - 4.36: 15685 4.36 - 4.90: 26632 Nonbonded interactions: 64549 Sorted by model distance: nonbonded pdb=" OG SER A1080 " pdb=" OD1 ASP A1081 " model vdw 2.187 2.440 nonbonded pdb=" O LEU A 551 " pdb=" OG1 THR A 554 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP A1040 " pdb=" N GLU A1041 " model vdw 2.241 2.520 nonbonded pdb=" O GLU A 543 " pdb=" OG SER A 547 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR B 418 " pdb=" OE1 GLU B 435 " model vdw 2.269 2.440 ... (remaining 64544 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 24.140 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 26.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.003 0.031 8780 Z= 0.193 Angle : 0.780 11.487 11905 Z= 0.392 Chirality : 0.046 0.164 1350 Planarity : 0.004 0.043 1515 Dihedral : 16.633 89.810 3272 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.21 % Allowed : 0.42 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.26), residues: 1067 helix: 0.08 (0.35), residues: 246 sheet: 0.28 (0.37), residues: 203 loop : -2.08 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 900 HIS 0.008 0.001 HIS B 430 PHE 0.026 0.002 PHE B 385 TYR 0.020 0.002 TYR A1186 ARG 0.020 0.001 ARG A 882 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 551 LEU cc_start: 0.7731 (mm) cc_final: 0.7458 (mt) REVERT: A 586 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7289 (mtp180) REVERT: A 607 MET cc_start: 0.6620 (mmm) cc_final: 0.6395 (mtt) REVERT: A 677 MET cc_start: 0.8016 (mmt) cc_final: 0.7815 (mmt) REVERT: A 1138 MET cc_start: 0.7502 (ttt) cc_final: 0.7211 (ttt) outliers start: 2 outliers final: 0 residues processed: 102 average time/residue: 0.1924 time to fit residues: 28.4619 Evaluate side-chains 84 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 GLN ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS B 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8780 Z= 0.385 Angle : 0.756 7.527 11905 Z= 0.389 Chirality : 0.050 0.176 1350 Planarity : 0.006 0.053 1515 Dihedral : 5.552 29.912 1177 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 1.68 % Allowed : 14.21 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.26), residues: 1067 helix: -0.53 (0.31), residues: 266 sheet: 0.14 (0.38), residues: 209 loop : -2.23 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 582 HIS 0.006 0.002 HIS A 928 PHE 0.024 0.002 PHE A 704 TYR 0.018 0.002 TYR A1186 ARG 0.006 0.001 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.032 Fit side-chains REVERT: A 661 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 677 MET cc_start: 0.8206 (mmt) cc_final: 0.7794 (mmt) REVERT: B 107 LEU cc_start: 0.7706 (mp) cc_final: 0.7475 (mt) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.1722 time to fit residues: 22.9343 Evaluate side-chains 85 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 ASN ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8780 Z= 0.222 Angle : 0.630 7.888 11905 Z= 0.321 Chirality : 0.046 0.146 1350 Planarity : 0.005 0.052 1515 Dihedral : 5.016 24.373 1173 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.89 % Allowed : 19.16 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.26), residues: 1067 helix: -0.06 (0.33), residues: 251 sheet: -0.02 (0.37), residues: 221 loop : -2.21 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 900 HIS 0.004 0.001 HIS A 663 PHE 0.020 0.002 PHE A 704 TYR 0.012 0.001 TYR A1145 ARG 0.003 0.000 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.083 Fit side-chains REVERT: A 661 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7295 (tm-30) REVERT: A 662 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8106 (t) REVERT: A 677 MET cc_start: 0.8156 (mmt) cc_final: 0.7784 (mmt) REVERT: B 107 LEU cc_start: 0.7778 (mp) cc_final: 0.7537 (mt) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.1795 time to fit residues: 25.5872 Evaluate side-chains 86 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8780 Z= 0.162 Angle : 0.596 9.514 11905 Z= 0.300 Chirality : 0.044 0.143 1350 Planarity : 0.004 0.050 1515 Dihedral : 4.771 23.227 1173 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 1.89 % Allowed : 21.37 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.26), residues: 1067 helix: -0.02 (0.34), residues: 255 sheet: -0.05 (0.37), residues: 219 loop : -2.14 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 900 HIS 0.003 0.001 HIS A1279 PHE 0.019 0.001 PHE A 704 TYR 0.014 0.001 TYR A 575 ARG 0.005 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.891 Fit side-chains REVERT: B 107 LEU cc_start: 0.7790 (mp) cc_final: 0.7553 (mt) outliers start: 18 outliers final: 13 residues processed: 96 average time/residue: 0.1684 time to fit residues: 24.6097 Evaluate side-chains 92 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8780 Z= 0.219 Angle : 0.607 7.875 11905 Z= 0.310 Chirality : 0.044 0.144 1350 Planarity : 0.005 0.050 1515 Dihedral : 4.809 23.072 1173 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.37 % Allowed : 21.26 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.26), residues: 1067 helix: 0.05 (0.33), residues: 259 sheet: -0.12 (0.37), residues: 213 loop : -2.28 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 900 HIS 0.005 0.001 HIS A 663 PHE 0.020 0.002 PHE A 704 TYR 0.016 0.001 TYR A 575 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 1.062 Fit side-chains REVERT: A 661 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 677 MET cc_start: 0.8217 (mmt) cc_final: 0.7825 (mmt) outliers start: 32 outliers final: 23 residues processed: 107 average time/residue: 0.1746 time to fit residues: 27.8524 Evaluate side-chains 103 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.0010 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8780 Z= 0.135 Angle : 0.592 11.633 11905 Z= 0.292 Chirality : 0.043 0.144 1350 Planarity : 0.004 0.048 1515 Dihedral : 4.574 22.614 1173 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.84 % Allowed : 22.53 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.26), residues: 1067 helix: 0.05 (0.34), residues: 263 sheet: -0.06 (0.38), residues: 213 loop : -2.18 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 900 HIS 0.013 0.001 HIS A1178 PHE 0.018 0.001 PHE A 704 TYR 0.012 0.001 TYR A 575 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 0.976 Fit side-chains REVERT: A 661 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 677 MET cc_start: 0.8144 (mmt) cc_final: 0.7646 (mmt) REVERT: B 305 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7476 (mp) outliers start: 27 outliers final: 18 residues processed: 108 average time/residue: 0.1689 time to fit residues: 27.2543 Evaluate side-chains 98 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.0270 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8780 Z= 0.127 Angle : 0.576 10.251 11905 Z= 0.284 Chirality : 0.043 0.138 1350 Planarity : 0.004 0.047 1515 Dihedral : 4.424 21.406 1173 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.63 % Allowed : 23.05 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.26), residues: 1067 helix: 0.15 (0.34), residues: 264 sheet: -0.04 (0.38), residues: 213 loop : -2.13 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 900 HIS 0.002 0.000 HIS A1279 PHE 0.018 0.001 PHE A 704 TYR 0.011 0.001 TYR A1145 ARG 0.007 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 551 LEU cc_start: 0.7395 (mm) cc_final: 0.7167 (mt) REVERT: A 661 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 305 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7499 (mp) outliers start: 25 outliers final: 17 residues processed: 112 average time/residue: 0.1727 time to fit residues: 29.0533 Evaluate side-chains 101 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8780 Z= 0.157 Angle : 0.611 10.305 11905 Z= 0.299 Chirality : 0.043 0.139 1350 Planarity : 0.004 0.047 1515 Dihedral : 4.416 21.132 1173 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.05 % Allowed : 23.68 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.26), residues: 1067 helix: 0.18 (0.34), residues: 264 sheet: -0.05 (0.38), residues: 213 loop : -2.12 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 900 HIS 0.004 0.001 HIS A1178 PHE 0.018 0.001 PHE A 704 TYR 0.012 0.001 TYR A 575 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 1.113 Fit side-chains REVERT: A 551 LEU cc_start: 0.7450 (mm) cc_final: 0.7211 (mt) REVERT: A 661 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7094 (tm-30) REVERT: B 305 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7479 (mp) outliers start: 29 outliers final: 24 residues processed: 111 average time/residue: 0.1789 time to fit residues: 29.5170 Evaluate side-chains 108 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 718 HIS Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 420 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8780 Z= 0.142 Angle : 0.605 13.291 11905 Z= 0.296 Chirality : 0.043 0.141 1350 Planarity : 0.004 0.046 1515 Dihedral : 4.382 21.132 1173 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.16 % Allowed : 23.05 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.26), residues: 1067 helix: 0.08 (0.34), residues: 270 sheet: -0.02 (0.38), residues: 213 loop : -2.10 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 900 HIS 0.002 0.001 HIS B 430 PHE 0.018 0.001 PHE A 704 TYR 0.012 0.001 TYR A 575 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 551 LEU cc_start: 0.7356 (mm) cc_final: 0.7108 (mt) REVERT: A 598 GLU cc_start: 0.7075 (tp30) cc_final: 0.6178 (tm-30) REVERT: A 661 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7488 (tm-30) REVERT: B 305 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7494 (mp) outliers start: 30 outliers final: 25 residues processed: 109 average time/residue: 0.1787 time to fit residues: 28.9823 Evaluate side-chains 109 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1246 PHE Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 0.0670 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS B 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8780 Z= 0.212 Angle : 0.638 12.570 11905 Z= 0.315 Chirality : 0.044 0.143 1350 Planarity : 0.004 0.047 1515 Dihedral : 4.498 20.815 1173 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.74 % Allowed : 23.79 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.26), residues: 1067 helix: 0.12 (0.34), residues: 268 sheet: -0.07 (0.38), residues: 213 loop : -2.16 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 900 HIS 0.006 0.001 HIS A1178 PHE 0.019 0.002 PHE A 704 TYR 0.013 0.001 TYR A 575 ARG 0.004 0.000 ARG A 621 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 598 GLU cc_start: 0.7036 (tp30) cc_final: 0.6135 (tm-30) REVERT: A 677 MET cc_start: 0.8213 (mmt) cc_final: 0.7765 (mmt) outliers start: 26 outliers final: 25 residues processed: 104 average time/residue: 0.1716 time to fit residues: 27.8412 Evaluate side-chains 105 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.110431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098288 restraints weight = 18760.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100810 restraints weight = 9842.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102453 restraints weight = 6105.225| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8780 Z= 0.288 Angle : 0.682 12.077 11905 Z= 0.344 Chirality : 0.046 0.147 1350 Planarity : 0.005 0.048 1515 Dihedral : 4.818 21.928 1173 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 3.05 % Allowed : 23.58 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.26), residues: 1067 helix: -0.05 (0.33), residues: 265 sheet: -0.17 (0.37), residues: 214 loop : -2.32 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 900 HIS 0.008 0.001 HIS A1178 PHE 0.020 0.002 PHE A 704 TYR 0.013 0.002 TYR A 575 ARG 0.003 0.000 ARG A 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.75 seconds wall clock time: 37 minutes 58.47 seconds (2278.47 seconds total)