Starting phenix.real_space_refine on Sat Feb 17 04:00:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxd_23570/02_2024/7lxd_23570_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxd_23570/02_2024/7lxd_23570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxd_23570/02_2024/7lxd_23570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxd_23570/02_2024/7lxd_23570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxd_23570/02_2024/7lxd_23570_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxd_23570/02_2024/7lxd_23570_updated.pdb" } resolution = 4.11 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= 1.000 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 Fe 4 7.16 5 S 83 5.16 5 C 11249 2.51 5 N 2898 2.21 5 O 3222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 599": "OD1" <-> "OD2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A ASP 1070": "OD1" <-> "OD2" Residue "A PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A ASP 1144": "OD1" <-> "OD2" Residue "A PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1195": "NH1" <-> "NH2" Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1435": "NH1" <-> "NH2" Residue "A GLU 1483": "OE1" <-> "OE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 64": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ASP 64": "OD1" <-> "OD2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 25": "NH1" <-> "NH2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ASP 265": "OD1" <-> "OD2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F ASP 362": "OD1" <-> "OD2" Residue "F ASP 414": "OD1" <-> "OD2" Residue "F TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "G TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17456 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9725 Classifications: {'peptide': 1190} Link IDs: {'PTRANS': 56, 'TRANS': 1133} Chain breaks: 10 Chain: "D" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1364 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain breaks: 2 Chain: "E" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1718 Classifications: {'peptide': 205} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3668 Classifications: {'peptide': 459} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 429} Chain breaks: 3 Chain: "G" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 973 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9591 SG CYS A1473 44.489 79.651 84.983 1.00123.06 S ATOM 9403 SG CYS A1449 39.309 82.759 85.540 1.00111.91 S ATOM 9379 SG CYS A1446 43.965 84.368 80.827 1.00106.48 S ATOM 9551 SG CYS A1468 45.400 84.939 86.732 1.00115.48 S Time building chain proxies: 9.25, per 1000 atoms: 0.53 Number of scatterers: 17456 At special positions: 0 Unit cell: (86.478, 143.136, 168.483, 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) Fe 4 26.01 S 83 16.00 O 3222 8.00 N 2898 7.00 C 11249 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: 6.45 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1601 " pdb="FE4 SF4 A1601 " - pdb=" SG CYS A1468 " pdb="FE2 SF4 A1601 " - pdb=" SG CYS A1449 " pdb="FE3 SF4 A1601 " - pdb=" SG CYS A1446 " pdb="FE1 SF4 A1601 " - pdb=" SG CYS A1473 " Number of angles added : 12 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 12 sheets defined 31.8% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 92 through 95 No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.788A pdb=" N ILE A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 613 through 624 Proline residue: A 624 - end of helix Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.689A pdb=" N ILE A 730 " --> pdb=" O PHE A 726 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A 732 " --> pdb=" O THR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 758 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 790 through 793 No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 837 through 839 No H-bonds generated for 'chain 'A' and resid 837 through 839' Processing helix chain 'A' and resid 844 through 847 No H-bonds generated for 'chain 'A' and resid 844 through 847' Processing helix chain 'A' and resid 858 through 864 Processing helix chain 'A' and resid 871 through 894 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.870A pdb=" N TYR A 916 " --> pdb=" O PHE A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 934 Processing helix chain 'A' and resid 944 through 947 No H-bonds generated for 'chain 'A' and resid 944 through 947' Processing helix chain 'A' and resid 980 through 987 Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 1022 through 1024 No H-bonds generated for 'chain 'A' and resid 1022 through 1024' Processing helix chain 'A' and resid 1045 through 1066 Processing helix chain 'A' and resid 1075 through 1091 removed outlier: 4.307A pdb=" N VAL A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1129 Processing helix chain 'A' and resid 1158 through 1172 removed outlier: 4.046A pdb=" N HIS A1163 " --> pdb=" O PHE A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1240 Processing helix chain 'A' and resid 1245 through 1259 Processing helix chain 'A' and resid 1336 through 1338 No H-bonds generated for 'chain 'A' and resid 1336 through 1338' Processing helix chain 'A' and resid 1345 through 1357 Proline residue: A1353 - end of helix removed outlier: 3.501A pdb=" N ARG A1357 " --> pdb=" O PRO A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1362 No H-bonds generated for 'chain 'A' and resid 1359 through 1362' Processing helix chain 'A' and resid 1366 through 1375 removed outlier: 4.262A pdb=" N LYS A1375 " --> pdb=" O GLN A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1452 removed outlier: 5.106A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1466 Processing helix chain 'A' and resid 1476 through 1485 Processing helix chain 'D' and resid 6 through 23 Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.995A pdb=" N ARG D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 23 Processing helix chain 'E' and resid 52 through 65 Processing helix chain 'E' and resid 99 through 102 No H-bonds generated for 'chain 'E' and resid 99 through 102' Processing helix chain 'E' and resid 110 through 129 Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.862A pdb=" N LEU E 156 " --> pdb=" O GLY E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'F' and resid 1 through 8 Processing helix chain 'F' and resid 52 through 70 removed outlier: 3.748A pdb=" N ILE F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 No H-bonds generated for 'chain 'F' and resid 93 through 96' Processing helix chain 'F' and resid 130 through 142 removed outlier: 4.430A pdb=" N TYR F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR F 137 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU F 140 " --> pdb=" O TYR F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.801A pdb=" N ARG F 163 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER F 164 " --> pdb=" O PHE F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 164' Processing helix chain 'F' and resid 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 273 through 290 removed outlier: 3.581A pdb=" N SER F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 330 removed outlier: 4.010A pdb=" N SER F 326 " --> pdb=" O LYS F 322 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR F 327 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 365 removed outlier: 4.581A pdb=" N ILE F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 405 removed outlier: 4.384A pdb=" N ASP F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 398 " --> pdb=" O HIS F 394 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET F 399 " --> pdb=" O ARG F 395 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU F 400 " --> pdb=" O LEU F 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 removed outlier: 4.246A pdb=" N PHE G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 29 Processing helix chain 'G' and resid 33 through 45 Processing sheet with id= A, first strand: chain 'A' and resid 30 through 35 removed outlier: 3.895A pdb=" N ASP A 31 " --> pdb=" O ARG A 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 693 through 696 removed outlier: 3.742A pdb=" N TRP A 696 " --> pdb=" O GLY A 713 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 713 " --> pdb=" O TRP A 696 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 971 through 973 removed outlier: 3.831A pdb=" N VAL A1148 " --> pdb=" O ILE A 972 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR A1149 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL A1138 " --> pdb=" O TYR A1149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1027 through 1029 Processing sheet with id= E, first strand: chain 'D' and resid 75 through 80 Processing sheet with id= F, first strand: chain 'E' and resid 32 through 35 Processing sheet with id= G, first strand: chain 'E' and resid 140 through 146 removed outlier: 3.573A pdb=" N ILE E 80 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 144 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 146 through 149 removed outlier: 3.959A pdb=" N ILE F 146 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 155 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 344 through 346 removed outlier: 6.286A pdb=" N VAL F 435 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR F 436 " --> pdb=" O ASN F 455 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS F 457 " --> pdb=" O TYR F 436 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL F 438 " --> pdb=" O LYS F 457 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE F 459 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN F 440 " --> pdb=" O ILE F 459 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL F 461 " --> pdb=" O ASN F 440 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 470 through 472 Processing sheet with id= K, first strand: chain 'F' and resid 104 through 109 removed outlier: 4.141A pdb=" N CYS F 104 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE F 175 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 108 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL F 171 " --> pdb=" O ILE F 108 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 56 through 58 434 hydrogen bonds defined for protein. 1275 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: 4.75 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 7460 1.43 - 1.64: 10270 1.64 - 1.86: 113 1.86 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 17855 Sorted by residual: bond pdb=" CA LYS A1214 " pdb=" C LYS A1214 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.24e-02 6.50e+03 1.64e+01 bond pdb=" C PRO A1353 " pdb=" N PRO A1354 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.20e-02 6.94e+03 1.20e+01 bond pdb=" C HIS A1186 " pdb=" N PRO A1187 " ideal model delta sigma weight residual 1.334 1.410 -0.076 2.34e-02 1.83e+03 1.06e+01 bond pdb=" C ASN F 199 " pdb=" N PRO F 200 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.12e-02 7.97e+03 5.94e+00 bond pdb=" N THR A1154 " pdb=" CA THR A1154 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.45e-02 4.76e+03 4.54e+00 ... (remaining 17850 not shown) Histogram of bond angle deviations from ideal: 73.54 - 86.26: 12 86.26 - 98.97: 4 98.97 - 111.69: 7465 111.69 - 124.41: 16172 124.41 - 137.12: 509 Bond angle restraints: 24162 Sorted by residual: angle pdb=" CG1 ILE A 709 " pdb=" CB ILE A 709 " pdb=" CG2 ILE A 709 " ideal model delta sigma weight residual 110.70 91.53 19.17 3.00e+00 1.11e-01 4.08e+01 angle pdb=" C GLY A1215 " pdb=" N ILE A1216 " pdb=" CA ILE A1216 " ideal model delta sigma weight residual 120.49 128.78 -8.29 1.38e+00 5.25e-01 3.61e+01 angle pdb=" CA LEU F 478 " pdb=" CB LEU F 478 " pdb=" CG LEU F 478 " ideal model delta sigma weight residual 116.30 137.12 -20.82 3.50e+00 8.16e-02 3.54e+01 angle pdb=" N GLU G 11 " pdb=" CA GLU G 11 " pdb=" CB GLU G 11 " ideal model delta sigma weight residual 110.07 118.67 -8.60 1.45e+00 4.76e-01 3.52e+01 angle pdb=" C GLY A1094 " pdb=" N TYR A1095 " pdb=" CA TYR A1095 " ideal model delta sigma weight residual 121.54 132.07 -10.53 1.91e+00 2.74e-01 3.04e+01 ... (remaining 24157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 9425 17.43 - 34.86: 1131 34.86 - 52.29: 208 52.29 - 69.71: 30 69.71 - 87.14: 16 Dihedral angle restraints: 10810 sinusoidal: 4493 harmonic: 6317 Sorted by residual: dihedral pdb=" CA ARG F 25 " pdb=" C ARG F 25 " pdb=" N VAL F 26 " pdb=" CA VAL F 26 " ideal model delta harmonic sigma weight residual 180.00 105.34 74.66 0 5.00e+00 4.00e-02 2.23e+02 dihedral pdb=" CA ASP F 414 " pdb=" C ASP F 414 " pdb=" N THR F 415 " pdb=" CA THR F 415 " ideal model delta harmonic sigma weight residual 180.00 122.17 57.83 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA TYR A1196 " pdb=" C TYR A1196 " pdb=" N VAL A1197 " pdb=" CA VAL A1197 " ideal model delta harmonic sigma weight residual -180.00 -124.51 -55.49 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 10807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2345 0.104 - 0.209: 302 0.209 - 0.313: 32 0.313 - 0.418: 9 0.418 - 0.522: 3 Chirality restraints: 2691 Sorted by residual: chirality pdb=" CB ILE E 108 " pdb=" CA ILE E 108 " pdb=" CG1 ILE E 108 " pdb=" CG2 ILE E 108 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CG LEU D 202 " pdb=" CB LEU D 202 " pdb=" CD1 LEU D 202 " pdb=" CD2 LEU D 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB VAL F 438 " pdb=" CA VAL F 438 " pdb=" CG1 VAL F 438 " pdb=" CG2 VAL F 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 2688 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 961 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 962 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 962 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 962 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1213 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ALA A1213 " -0.067 2.00e-02 2.50e+03 pdb=" O ALA A1213 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A1214 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1173 " -0.063 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO A1174 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A1174 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1174 " -0.051 5.00e-02 4.00e+02 ... (remaining 3061 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4280 2.80 - 3.33: 16922 3.33 - 3.85: 30778 3.85 - 4.38: 34680 4.38 - 4.90: 56547 Nonbonded interactions: 143207 Sorted by model distance: nonbonded pdb=" O ILE A 78 " pdb=" OH TYR A 195 " model vdw 2.276 2.440 nonbonded pdb=" O ASP A 139 " pdb=" OG SER A 162 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 149 " pdb=" O LEU A1008 " model vdw 2.277 2.440 nonbonded pdb=" O SER A1047 " pdb=" OG1 THR A1051 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR A 668 " pdb=" O ASP A 760 " model vdw 2.284 2.440 ... (remaining 143202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.770 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: 3.370 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 48.890 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 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 : 0.006 0.087 17855 Z= 0.373 Angle : 1.303 20.821 24162 Z= 0.693 Chirality : 0.074 0.522 2691 Planarity : 0.009 0.103 3064 Dihedral : 15.453 87.143 6708 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.94 % Twisted General : 0.65 % 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: -3.73 (0.16), residues: 2093 helix: -1.88 (0.17), residues: 685 sheet: -2.88 (0.34), residues: 179 loop : -2.88 (0.15), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 155 HIS 0.008 0.001 HIS A 105 PHE 0.039 0.003 PHE A1199 TYR 0.035 0.003 TYR A1201 ARG 0.019 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6726 (ptp) cc_final: 0.6489 (ptt) REVERT: A 84 ILE cc_start: 0.5036 (pt) cc_final: 0.4778 (pt) REVERT: A 240 LEU cc_start: 0.9085 (mm) cc_final: 0.8250 (tt) REVERT: A 530 TYR cc_start: 0.5956 (t80) cc_final: 0.5578 (t80) REVERT: A 532 ASP cc_start: 0.7476 (p0) cc_final: 0.6716 (t0) REVERT: A 618 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8640 (mmmm) REVERT: A 872 THR cc_start: 0.8702 (p) cc_final: 0.8249 (t) REVERT: A 912 PHE cc_start: 0.8018 (t80) cc_final: 0.7764 (t80) REVERT: A 1043 LYS cc_start: 0.7598 (ttpt) cc_final: 0.7157 (tptt) REVERT: A 1076 ARG cc_start: 0.8844 (ptt90) cc_final: 0.8316 (ptt-90) REVERT: A 1080 ASN cc_start: 0.7803 (p0) cc_final: 0.7494 (p0) REVERT: A 1156 ILE cc_start: 0.8530 (tt) cc_final: 0.8314 (tp) REVERT: A 1232 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 1251 LEU cc_start: 0.8937 (mm) cc_final: 0.8552 (mt) REVERT: D 64 ASP cc_start: 0.8090 (m-30) cc_final: 0.7476 (m-30) REVERT: D 124 LEU cc_start: 0.9382 (tp) cc_final: 0.9172 (tp) REVERT: D 126 MET cc_start: 0.6281 (tpp) cc_final: 0.5954 (mmp) REVERT: D 142 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6253 (tm-30) REVERT: E 40 PHE cc_start: 0.5983 (m-10) cc_final: 0.5781 (m-80) REVERT: E 66 LEU cc_start: 0.9071 (mt) cc_final: 0.8710 (pp) REVERT: F 226 SER cc_start: 0.5230 (m) cc_final: 0.5014 (m) REVERT: F 277 MET cc_start: 0.8185 (mpp) cc_final: 0.7476 (mpp) REVERT: F 288 HIS cc_start: 0.6171 (t-90) cc_final: 0.5936 (t70) REVERT: G 46 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8022 (pp30) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.3570 time to fit residues: 180.5537 Evaluate side-chains 211 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.2980 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 165 ASN A 224 ASN A 263 ASN A 617 GLN A 677 ASN A 731 GLN A 838 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1338 ASN A1371 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17855 Z= 0.222 Angle : 0.701 11.403 24162 Z= 0.366 Chirality : 0.046 0.180 2691 Planarity : 0.006 0.067 3064 Dihedral : 7.183 49.038 2308 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.75 % Favored : 90.16 % Rotamer: Outliers : 0.25 % Allowed : 6.88 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.97 % Twisted General : 0.25 % 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: -2.98 (0.17), residues: 2093 helix: -0.90 (0.18), residues: 702 sheet: -2.79 (0.33), residues: 178 loop : -2.62 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1134 HIS 0.004 0.001 HIS A 770 PHE 0.025 0.002 PHE F 464 TYR 0.018 0.002 TYR A1346 ARG 0.007 0.001 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 269 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.5117 (pt) cc_final: 0.4897 (pt) REVERT: A 86 TYR cc_start: 0.6274 (p90) cc_final: 0.6056 (p90) REVERT: A 369 ASN cc_start: 0.4809 (m-40) cc_final: 0.4547 (m110) REVERT: A 372 ASN cc_start: 0.7452 (m110) cc_final: 0.7212 (m110) REVERT: A 530 TYR cc_start: 0.5792 (t80) cc_final: 0.5002 (t80) REVERT: A 532 ASP cc_start: 0.7681 (p0) cc_final: 0.6855 (t0) REVERT: A 593 TYR cc_start: 0.7820 (p90) cc_final: 0.7466 (p90) REVERT: A 595 LYS cc_start: 0.8791 (tmmt) cc_final: 0.8563 (tmmt) REVERT: A 911 ASP cc_start: 0.6231 (p0) cc_final: 0.5801 (p0) REVERT: A 912 PHE cc_start: 0.8145 (t80) cc_final: 0.7725 (t80) REVERT: A 1043 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7264 (tptt) REVERT: A 1076 ARG cc_start: 0.8754 (ptt90) cc_final: 0.8473 (ptt-90) REVERT: A 1146 LEU cc_start: 0.7452 (tp) cc_final: 0.7239 (tp) REVERT: A 1191 ILE cc_start: 0.6373 (tt) cc_final: 0.6049 (tt) REVERT: A 1208 LEU cc_start: 0.8042 (tp) cc_final: 0.7824 (tp) REVERT: A 1232 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 1251 LEU cc_start: 0.8855 (mm) cc_final: 0.8560 (mt) REVERT: D 124 LEU cc_start: 0.9437 (tp) cc_final: 0.9188 (tp) REVERT: D 126 MET cc_start: 0.6851 (tpp) cc_final: 0.6399 (mmt) REVERT: D 142 GLU cc_start: 0.6630 (tm-30) cc_final: 0.5894 (tm-30) REVERT: D 196 LYS cc_start: 0.1587 (tptt) cc_final: 0.1200 (tptt) REVERT: E 66 LEU cc_start: 0.9453 (mt) cc_final: 0.8801 (pp) REVERT: E 71 HIS cc_start: 0.6054 (OUTLIER) cc_final: 0.5846 (m90) REVERT: E 158 ARG cc_start: 0.5694 (mpt180) cc_final: 0.3539 (mmt-90) REVERT: F 257 LEU cc_start: 0.8592 (tp) cc_final: 0.8197 (tp) REVERT: G 46 GLN cc_start: 0.8423 (mm-40) cc_final: 0.7880 (pp30) outliers start: 5 outliers final: 0 residues processed: 272 average time/residue: 0.3147 time to fit residues: 127.5375 Evaluate side-chains 185 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 0.0670 chunk 59 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 190 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 GLN ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN D 214 GLN E 2 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17855 Z= 0.181 Angle : 0.673 11.204 24162 Z= 0.346 Chirality : 0.046 0.184 2691 Planarity : 0.006 0.076 3064 Dihedral : 6.709 49.578 2308 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.84 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.97 % Twisted General : 0.25 % 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: -2.79 (0.17), residues: 2093 helix: -0.68 (0.18), residues: 702 sheet: -2.81 (0.34), residues: 175 loop : -2.53 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 827 HIS 0.009 0.001 HIS F 288 PHE 0.018 0.001 PHE F 328 TYR 0.022 0.002 TYR D 91 ARG 0.007 0.000 ARG A 948 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.9005 (mm) cc_final: 0.8398 (tp) REVERT: A 530 TYR cc_start: 0.5911 (t80) cc_final: 0.5197 (t80) REVERT: A 595 LYS cc_start: 0.8737 (tmmt) cc_final: 0.8530 (tmmt) REVERT: A 740 MET cc_start: 0.5202 (mpp) cc_final: 0.4932 (mpp) REVERT: A 903 GLU cc_start: 0.6950 (mp0) cc_final: 0.6477 (mp0) REVERT: A 912 PHE cc_start: 0.7991 (t80) cc_final: 0.7676 (t80) REVERT: A 948 ARG cc_start: 0.6819 (mmp80) cc_final: 0.6568 (mpt180) REVERT: A 1022 LEU cc_start: 0.8363 (mp) cc_final: 0.7766 (tt) REVERT: A 1043 LYS cc_start: 0.7427 (ttpt) cc_final: 0.6907 (tppt) REVERT: A 1049 MET cc_start: 0.8046 (mtm) cc_final: 0.7757 (mtp) REVERT: A 1064 MET cc_start: 0.7890 (ptt) cc_final: 0.7620 (ptm) REVERT: A 1076 ARG cc_start: 0.8891 (ptt90) cc_final: 0.8665 (ttp-170) REVERT: A 1146 LEU cc_start: 0.7239 (tp) cc_final: 0.6951 (tp) REVERT: A 1208 LEU cc_start: 0.8150 (tp) cc_final: 0.7908 (tp) REVERT: A 1232 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 1251 LEU cc_start: 0.8830 (mm) cc_final: 0.8447 (mm) REVERT: D 9 LEU cc_start: 0.9122 (tt) cc_final: 0.8900 (tt) REVERT: D 126 MET cc_start: 0.6777 (tpp) cc_final: 0.6270 (mmt) REVERT: D 142 GLU cc_start: 0.6136 (tm-30) cc_final: 0.5620 (tm-30) REVERT: D 196 LYS cc_start: 0.1563 (tptt) cc_final: 0.1122 (tptt) REVERT: E 16 TYR cc_start: 0.7900 (t80) cc_final: 0.7226 (t80) REVERT: E 66 LEU cc_start: 0.9387 (mt) cc_final: 0.8824 (pp) REVERT: E 158 ARG cc_start: 0.5623 (mpt180) cc_final: 0.4572 (mmt-90) REVERT: F 257 LEU cc_start: 0.8474 (tp) cc_final: 0.8061 (tp) REVERT: G 46 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7895 (pp30) REVERT: G 63 GLN cc_start: 0.7021 (tt0) cc_final: 0.6752 (tm-30) REVERT: G 115 LEU cc_start: 0.7350 (mp) cc_final: 0.6687 (mt) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3480 time to fit residues: 141.5523 Evaluate side-chains 181 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 91 optimal weight: 0.0570 chunk 128 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 531 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17855 Z= 0.242 Angle : 0.704 10.097 24162 Z= 0.365 Chirality : 0.047 0.237 2691 Planarity : 0.005 0.058 3064 Dihedral : 6.573 48.554 2308 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.22 % Favored : 89.73 % Rotamer: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 (0.17), residues: 2093 helix: -0.50 (0.19), residues: 697 sheet: -2.80 (0.34), residues: 164 loop : -2.50 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 405 HIS 0.006 0.001 HIS A 105 PHE 0.030 0.002 PHE F 464 TYR 0.041 0.002 TYR D 91 ARG 0.023 0.001 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6143 (p90) cc_final: 0.5901 (p90) REVERT: A 239 GLN cc_start: 0.7758 (mp10) cc_final: 0.7193 (tp-100) REVERT: A 240 LEU cc_start: 0.8914 (mm) cc_final: 0.8692 (mm) REVERT: A 579 THR cc_start: 0.7556 (m) cc_final: 0.7259 (p) REVERT: A 614 ASP cc_start: 0.7918 (m-30) cc_final: 0.7551 (m-30) REVERT: A 912 PHE cc_start: 0.8249 (t80) cc_final: 0.8006 (t80) REVERT: A 1043 LYS cc_start: 0.7472 (ttpt) cc_final: 0.7104 (tptt) REVERT: A 1064 MET cc_start: 0.8255 (ptt) cc_final: 0.7936 (ptm) REVERT: A 1076 ARG cc_start: 0.8967 (ptt90) cc_final: 0.8720 (ttp-170) REVERT: A 1146 LEU cc_start: 0.6973 (tp) cc_final: 0.6731 (tp) REVERT: A 1234 CYS cc_start: 0.8583 (t) cc_final: 0.7985 (m) REVERT: A 1368 ASN cc_start: 0.8270 (t0) cc_final: 0.7797 (m-40) REVERT: D 64 ASP cc_start: 0.8454 (m-30) cc_final: 0.7917 (t70) REVERT: D 126 MET cc_start: 0.6527 (tpp) cc_final: 0.6068 (mmt) REVERT: E 66 LEU cc_start: 0.9315 (mt) cc_final: 0.8879 (pp) REVERT: E 71 HIS cc_start: 0.6228 (OUTLIER) cc_final: 0.5989 (m90) REVERT: F 151 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6530 (tm-30) REVERT: F 257 LEU cc_start: 0.8329 (tp) cc_final: 0.7985 (tp) REVERT: G 42 ASP cc_start: 0.8364 (t70) cc_final: 0.8127 (t0) REVERT: G 46 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8029 (pp30) REVERT: G 63 GLN cc_start: 0.7341 (tt0) cc_final: 0.7020 (tm-30) outliers start: 2 outliers final: 0 residues processed: 248 average time/residue: 0.3064 time to fit residues: 116.0368 Evaluate side-chains 179 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 174 optimal weight: 0.0670 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1259 GLN A1338 ASN A1371 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS E 213 HIS ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17855 Z= 0.206 Angle : 0.680 10.331 24162 Z= 0.350 Chirality : 0.047 0.233 2691 Planarity : 0.005 0.074 3064 Dihedral : 6.477 47.984 2308 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.89 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.64 (0.17), residues: 2093 helix: -0.40 (0.19), residues: 694 sheet: -2.96 (0.31), residues: 185 loop : -2.48 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1134 HIS 0.006 0.001 HIS F 288 PHE 0.026 0.002 PHE F 464 TYR 0.024 0.002 TYR D 91 ARG 0.005 0.000 ARG E 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6104 (p90) cc_final: 0.5719 (p90) REVERT: A 239 GLN cc_start: 0.7503 (mp10) cc_final: 0.7057 (tp-100) REVERT: A 240 LEU cc_start: 0.8873 (mm) cc_final: 0.8583 (mm) REVERT: A 369 ASN cc_start: 0.6360 (m110) cc_final: 0.5969 (m110) REVERT: A 530 TYR cc_start: 0.5815 (t80) cc_final: 0.5162 (t80) REVERT: A 579 THR cc_start: 0.7594 (m) cc_final: 0.7298 (p) REVERT: A 614 ASP cc_start: 0.7733 (m-30) cc_final: 0.7481 (m-30) REVERT: A 912 PHE cc_start: 0.8313 (t80) cc_final: 0.8053 (t80) REVERT: A 984 MET cc_start: 0.5350 (mtm) cc_final: 0.5134 (mtm) REVERT: A 1043 LYS cc_start: 0.7415 (ttpt) cc_final: 0.7024 (tppt) REVERT: A 1049 MET cc_start: 0.8278 (mtp) cc_final: 0.7445 (mtp) REVERT: A 1076 ARG cc_start: 0.8995 (ptt90) cc_final: 0.8786 (ttp-170) REVERT: A 1251 LEU cc_start: 0.8950 (mm) cc_final: 0.8625 (mt) REVERT: A 1368 ASN cc_start: 0.8251 (t0) cc_final: 0.7781 (m-40) REVERT: D 64 ASP cc_start: 0.7692 (m-30) cc_final: 0.7397 (t70) REVERT: D 126 MET cc_start: 0.6575 (tpp) cc_final: 0.6135 (mmt) REVERT: E 66 LEU cc_start: 0.9534 (mt) cc_final: 0.8899 (pp) REVERT: E 158 ARG cc_start: 0.5716 (mpt180) cc_final: 0.4595 (mmt-90) REVERT: E 206 ASP cc_start: 0.7543 (m-30) cc_final: 0.6944 (m-30) REVERT: F 1 MET cc_start: 0.8807 (ppp) cc_final: 0.8495 (ppp) REVERT: F 151 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6575 (tm-30) REVERT: F 257 LEU cc_start: 0.8340 (tp) cc_final: 0.8079 (tp) REVERT: G 46 GLN cc_start: 0.8571 (mm-40) cc_final: 0.7989 (pp30) REVERT: G 63 GLN cc_start: 0.7478 (tt0) cc_final: 0.7103 (tm-30) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3071 time to fit residues: 113.1235 Evaluate side-chains 182 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 0.7980 chunk 183 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 288 HIS ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 213 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17855 Z= 0.218 Angle : 0.681 10.487 24162 Z= 0.352 Chirality : 0.047 0.250 2691 Planarity : 0.005 0.061 3064 Dihedral : 6.405 47.375 2308 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 0.05 % Allowed : 2.33 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.61 (0.17), residues: 2093 helix: -0.35 (0.19), residues: 699 sheet: -2.90 (0.32), residues: 185 loop : -2.49 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 394 HIS 0.008 0.001 HIS E 100 PHE 0.027 0.002 PHE F 464 TYR 0.018 0.002 TYR D 16 ARG 0.007 0.000 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.5704 (m-80) cc_final: 0.5393 (m-80) REVERT: A 86 TYR cc_start: 0.6210 (p90) cc_final: 0.5876 (p90) REVERT: A 239 GLN cc_start: 0.7619 (mp10) cc_final: 0.7088 (tp-100) REVERT: A 369 ASN cc_start: 0.6230 (m110) cc_final: 0.5945 (m110) REVERT: A 373 PHE cc_start: 0.6247 (t80) cc_final: 0.5916 (t80) REVERT: A 530 TYR cc_start: 0.5806 (t80) cc_final: 0.5177 (t80) REVERT: A 579 THR cc_start: 0.7319 (m) cc_final: 0.7113 (p) REVERT: A 614 ASP cc_start: 0.7750 (m-30) cc_final: 0.7507 (m-30) REVERT: A 911 ASP cc_start: 0.6665 (p0) cc_final: 0.6451 (p0) REVERT: A 912 PHE cc_start: 0.8284 (t80) cc_final: 0.7866 (t80) REVERT: A 984 MET cc_start: 0.5587 (mtm) cc_final: 0.5370 (mtm) REVERT: A 1022 LEU cc_start: 0.8643 (mt) cc_final: 0.8376 (tp) REVERT: A 1043 LYS cc_start: 0.7521 (ttpt) cc_final: 0.7043 (tppt) REVERT: A 1049 MET cc_start: 0.8399 (mtp) cc_final: 0.7628 (mmm) REVERT: A 1076 ARG cc_start: 0.9028 (ptt90) cc_final: 0.8788 (ttp-170) REVERT: A 1251 LEU cc_start: 0.8950 (mm) cc_final: 0.8667 (mm) REVERT: A 1368 ASN cc_start: 0.8206 (t0) cc_final: 0.7757 (m-40) REVERT: D 64 ASP cc_start: 0.7908 (m-30) cc_final: 0.7593 (t70) REVERT: D 126 MET cc_start: 0.6538 (tpp) cc_final: 0.6122 (mmt) REVERT: E 34 TYR cc_start: 0.6834 (m-80) cc_final: 0.6451 (m-80) REVERT: E 66 LEU cc_start: 0.9532 (mt) cc_final: 0.8872 (pp) REVERT: E 71 HIS cc_start: 0.6157 (OUTLIER) cc_final: 0.5895 (m90) REVERT: E 158 ARG cc_start: 0.5870 (mpt180) cc_final: 0.4805 (mmt-90) REVERT: E 206 ASP cc_start: 0.7655 (m-30) cc_final: 0.6972 (m-30) REVERT: F 151 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6641 (tm-30) REVERT: F 257 LEU cc_start: 0.7806 (tp) cc_final: 0.7422 (tp) REVERT: F 285 LYS cc_start: 0.8516 (tppt) cc_final: 0.8167 (tppp) REVERT: F 402 THR cc_start: 0.7597 (p) cc_final: 0.7391 (p) REVERT: G 42 ASP cc_start: 0.8356 (t70) cc_final: 0.8111 (t0) REVERT: G 46 GLN cc_start: 0.8608 (mm-40) cc_final: 0.7980 (pp30) REVERT: G 63 GLN cc_start: 0.7470 (tt0) cc_final: 0.6959 (tm-30) REVERT: G 107 LEU cc_start: 0.8677 (tp) cc_final: 0.8461 (tp) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.3327 time to fit residues: 122.2990 Evaluate side-chains 182 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 HIS ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17855 Z= 0.322 Angle : 0.782 11.073 24162 Z= 0.409 Chirality : 0.050 0.390 2691 Planarity : 0.006 0.059 3064 Dihedral : 6.817 47.140 2308 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.51 % Favored : 88.44 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.84 (0.17), residues: 2093 helix: -0.67 (0.18), residues: 714 sheet: -2.89 (0.32), residues: 187 loop : -2.59 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP F 405 HIS 0.008 0.002 HIS E 100 PHE 0.039 0.002 PHE F 464 TYR 0.053 0.002 TYR D 91 ARG 0.015 0.001 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6586 (p90) cc_final: 0.6304 (p90) REVERT: A 236 ASP cc_start: 0.8561 (t0) cc_final: 0.8307 (t0) REVERT: A 239 GLN cc_start: 0.7472 (mp10) cc_final: 0.7151 (tp-100) REVERT: A 355 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7914 (ttpp) REVERT: A 373 PHE cc_start: 0.6819 (t80) cc_final: 0.6346 (t80) REVERT: A 579 THR cc_start: 0.6932 (m) cc_final: 0.6681 (p) REVERT: A 614 ASP cc_start: 0.7696 (m-30) cc_final: 0.7458 (m-30) REVERT: A 863 ASN cc_start: 0.9014 (t0) cc_final: 0.8810 (t0) REVERT: A 984 MET cc_start: 0.5410 (mtm) cc_final: 0.5114 (mtm) REVERT: A 1022 LEU cc_start: 0.8655 (mt) cc_final: 0.8247 (tp) REVERT: A 1043 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7106 (tppt) REVERT: A 1049 MET cc_start: 0.8567 (mtp) cc_final: 0.7628 (mmm) REVERT: A 1064 MET cc_start: 0.8052 (ptt) cc_final: 0.7701 (ptm) REVERT: A 1076 ARG cc_start: 0.9088 (ptt90) cc_final: 0.8050 (tpp-160) REVERT: A 1173 ASN cc_start: 0.8619 (t0) cc_final: 0.8251 (m110) REVERT: A 1229 LYS cc_start: 0.8434 (tptt) cc_final: 0.8102 (mmmt) REVERT: A 1234 CYS cc_start: 0.8642 (t) cc_final: 0.7927 (m) REVERT: A 1251 LEU cc_start: 0.8933 (mm) cc_final: 0.8608 (mm) REVERT: A 1368 ASN cc_start: 0.8363 (t0) cc_final: 0.7960 (m-40) REVERT: D 126 MET cc_start: 0.6759 (tpp) cc_final: 0.6386 (mmt) REVERT: E 66 LEU cc_start: 0.9288 (mt) cc_final: 0.8895 (pp) REVERT: E 206 ASP cc_start: 0.7334 (m-30) cc_final: 0.6705 (m-30) REVERT: F 285 LYS cc_start: 0.8578 (tppt) cc_final: 0.8210 (tppp) REVERT: G 42 ASP cc_start: 0.8462 (t70) cc_final: 0.8141 (t0) REVERT: G 46 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7922 (pp30) REVERT: G 63 GLN cc_start: 0.8193 (tt0) cc_final: 0.7505 (tm-30) REVERT: G 69 HIS cc_start: 0.7601 (m-70) cc_final: 0.7024 (m170) REVERT: G 107 LEU cc_start: 0.8674 (tp) cc_final: 0.8178 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3189 time to fit residues: 112.9217 Evaluate side-chains 179 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 288 HIS ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 732 HIS A1172 ASN A1240 GLN A1338 ASN A1371 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17855 Z= 0.211 Angle : 0.716 10.611 24162 Z= 0.368 Chirality : 0.047 0.185 2691 Planarity : 0.005 0.057 3064 Dihedral : 6.511 44.320 2308 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.51 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.63 (0.18), residues: 2093 helix: -0.51 (0.19), residues: 705 sheet: -2.65 (0.33), residues: 191 loop : -2.46 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 405 HIS 0.007 0.001 HIS A 822 PHE 0.025 0.002 PHE A 349 TYR 0.024 0.002 TYR D 16 ARG 0.007 0.000 ARG E 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6209 (p90) cc_final: 0.5889 (p90) REVERT: A 236 ASP cc_start: 0.8523 (t0) cc_final: 0.8281 (t0) REVERT: A 373 PHE cc_start: 0.6317 (t80) cc_final: 0.6049 (t80) REVERT: A 530 TYR cc_start: 0.5547 (t80) cc_final: 0.5045 (t80) REVERT: A 579 THR cc_start: 0.6740 (m) cc_final: 0.6524 (p) REVERT: A 614 ASP cc_start: 0.7629 (m-30) cc_final: 0.7347 (m-30) REVERT: A 863 ASN cc_start: 0.9027 (t0) cc_final: 0.8805 (t0) REVERT: A 911 ASP cc_start: 0.6740 (p0) cc_final: 0.6423 (p0) REVERT: A 960 MET cc_start: 0.6470 (ppp) cc_final: 0.6265 (ppp) REVERT: A 984 MET cc_start: 0.5453 (mtm) cc_final: 0.5235 (mtm) REVERT: A 1043 LYS cc_start: 0.7427 (ttpt) cc_final: 0.6988 (tppt) REVERT: A 1049 MET cc_start: 0.8355 (mtp) cc_final: 0.7561 (mmm) REVERT: A 1064 MET cc_start: 0.7962 (ptt) cc_final: 0.7627 (ptm) REVERT: A 1229 LYS cc_start: 0.8356 (tptt) cc_final: 0.8070 (mmmt) REVERT: A 1234 CYS cc_start: 0.8418 (t) cc_final: 0.7727 (m) REVERT: A 1246 LYS cc_start: 0.8917 (mttt) cc_final: 0.8694 (mttt) REVERT: A 1251 LEU cc_start: 0.8942 (mm) cc_final: 0.8719 (mm) REVERT: A 1368 ASN cc_start: 0.8223 (t0) cc_final: 0.7757 (m-40) REVERT: D 126 MET cc_start: 0.6666 (tpp) cc_final: 0.6338 (mmt) REVERT: E 66 LEU cc_start: 0.9176 (mt) cc_final: 0.8848 (pp) REVERT: E 158 ARG cc_start: 0.6273 (mpt180) cc_final: 0.5713 (mpt180) REVERT: F 285 LYS cc_start: 0.8542 (tppt) cc_final: 0.8173 (tppp) REVERT: G 42 ASP cc_start: 0.8402 (t70) cc_final: 0.8064 (t0) REVERT: G 46 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7842 (pp30) REVERT: G 63 GLN cc_start: 0.7871 (tt0) cc_final: 0.7325 (tm-30) REVERT: G 69 HIS cc_start: 0.7765 (m-70) cc_final: 0.7222 (m170) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3500 time to fit residues: 129.7754 Evaluate side-chains 185 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 239 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 213 HIS ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17855 Z= 0.233 Angle : 0.714 10.820 24162 Z= 0.370 Chirality : 0.048 0.240 2691 Planarity : 0.005 0.055 3064 Dihedral : 6.438 43.320 2308 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 0.05 % Allowed : 1.47 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.55 (0.18), residues: 2093 helix: -0.37 (0.19), residues: 705 sheet: -2.83 (0.32), residues: 186 loop : -2.42 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1134 HIS 0.007 0.001 HIS A 822 PHE 0.028 0.002 PHE F 464 TYR 0.034 0.002 TYR D 91 ARG 0.007 0.001 ARG F 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6285 (p90) cc_final: 0.5997 (p90) REVERT: A 355 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7870 (ttpp) REVERT: A 593 TYR cc_start: 0.8053 (p90) cc_final: 0.7800 (p90) REVERT: A 614 ASP cc_start: 0.7581 (m-30) cc_final: 0.7341 (m-30) REVERT: A 716 ILE cc_start: 0.6172 (pt) cc_final: 0.5922 (pt) REVERT: A 863 ASN cc_start: 0.9094 (t0) cc_final: 0.8845 (t0) REVERT: A 911 ASP cc_start: 0.6757 (p0) cc_final: 0.6467 (p0) REVERT: A 912 PHE cc_start: 0.8172 (t80) cc_final: 0.7892 (t80) REVERT: A 960 MET cc_start: 0.6671 (ppp) cc_final: 0.6468 (ppp) REVERT: A 984 MET cc_start: 0.5647 (mtm) cc_final: 0.5384 (mtm) REVERT: A 1043 LYS cc_start: 0.7476 (ttpt) cc_final: 0.7158 (ttpt) REVERT: A 1049 MET cc_start: 0.8418 (mtp) cc_final: 0.7588 (mmm) REVERT: A 1064 MET cc_start: 0.8016 (ptt) cc_final: 0.7656 (ptm) REVERT: A 1076 ARG cc_start: 0.8851 (ptt-90) cc_final: 0.7943 (tpp-160) REVERT: A 1229 LYS cc_start: 0.8383 (tptt) cc_final: 0.8097 (mmmt) REVERT: A 1234 CYS cc_start: 0.8436 (t) cc_final: 0.7762 (m) REVERT: A 1246 LYS cc_start: 0.8973 (mttt) cc_final: 0.8754 (mttt) REVERT: D 124 LEU cc_start: 0.9431 (mt) cc_final: 0.9193 (mt) REVERT: D 126 MET cc_start: 0.6470 (tpp) cc_final: 0.6119 (mmt) REVERT: E 66 LEU cc_start: 0.9343 (mt) cc_final: 0.8895 (pp) REVERT: E 158 ARG cc_start: 0.6335 (mpt180) cc_final: 0.4931 (mmt-90) REVERT: F 285 LYS cc_start: 0.8578 (tppt) cc_final: 0.8184 (tppp) REVERT: G 46 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7854 (pp30) REVERT: G 63 GLN cc_start: 0.8122 (tt0) cc_final: 0.7399 (tm-30) REVERT: G 69 HIS cc_start: 0.7773 (m-70) cc_final: 0.7253 (m170) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.3191 time to fit residues: 112.2516 Evaluate side-chains 181 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 193 optimal weight: 0.0040 chunk 167 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 213 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17855 Z= 0.210 Angle : 0.722 11.308 24162 Z= 0.368 Chirality : 0.048 0.233 2691 Planarity : 0.005 0.066 3064 Dihedral : 6.265 41.724 2308 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 0.05 % Allowed : 0.66 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.55 (0.18), residues: 2093 helix: -0.46 (0.19), residues: 706 sheet: -2.63 (0.33), residues: 191 loop : -2.40 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 394 HIS 0.008 0.001 HIS E 100 PHE 0.023 0.002 PHE E 114 TYR 0.024 0.002 TYR D 91 ARG 0.007 0.000 ARG F 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7457 (m-30) cc_final: 0.7213 (m-30) REVERT: A 863 ASN cc_start: 0.9090 (t0) cc_final: 0.8856 (t0) REVERT: A 911 ASP cc_start: 0.6571 (p0) cc_final: 0.6316 (p0) REVERT: A 912 PHE cc_start: 0.8079 (t80) cc_final: 0.7791 (t80) REVERT: A 960 MET cc_start: 0.6461 (ppp) cc_final: 0.6255 (ppp) REVERT: A 984 MET cc_start: 0.5574 (mtm) cc_final: 0.5320 (mtm) REVERT: A 1043 LYS cc_start: 0.7305 (ttpt) cc_final: 0.7039 (ttpt) REVERT: A 1049 MET cc_start: 0.8384 (mtp) cc_final: 0.7555 (mmm) REVERT: A 1064 MET cc_start: 0.7997 (ptt) cc_final: 0.7625 (ptm) REVERT: A 1076 ARG cc_start: 0.8806 (ptt-90) cc_final: 0.7932 (tpp-160) REVERT: A 1234 CYS cc_start: 0.8391 (t) cc_final: 0.7742 (m) REVERT: A 1368 ASN cc_start: 0.8645 (m110) cc_final: 0.8419 (m-40) REVERT: D 112 GLU cc_start: 0.7585 (pm20) cc_final: 0.7322 (pm20) REVERT: D 124 LEU cc_start: 0.9442 (mt) cc_final: 0.9145 (mt) REVERT: D 126 MET cc_start: 0.6405 (tpp) cc_final: 0.5890 (mmt) REVERT: E 3 ARG cc_start: 0.8374 (tmm160) cc_final: 0.7547 (ttp80) REVERT: E 66 LEU cc_start: 0.9196 (mt) cc_final: 0.8776 (pp) REVERT: F 285 LYS cc_start: 0.8573 (tppt) cc_final: 0.8234 (tppp) REVERT: F 399 MET cc_start: 0.7562 (ttt) cc_final: 0.6972 (ptp) REVERT: G 46 GLN cc_start: 0.8579 (mm-40) cc_final: 0.7910 (pp30) REVERT: G 63 GLN cc_start: 0.7784 (tt0) cc_final: 0.7203 (tm-30) REVERT: G 69 HIS cc_start: 0.7843 (m-70) cc_final: 0.7134 (m170) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.3064 time to fit residues: 110.2560 Evaluate side-chains 178 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 154 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 213 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.100499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.088509 restraints weight = 80629.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.090595 restraints weight = 53232.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.092099 restraints weight = 38600.473| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17855 Z= 0.193 Angle : 0.700 10.733 24162 Z= 0.356 Chirality : 0.048 0.228 2691 Planarity : 0.005 0.054 3064 Dihedral : 6.159 38.532 2308 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.18), residues: 2093 helix: -0.33 (0.19), residues: 696 sheet: -2.64 (0.33), residues: 193 loop : -2.40 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 394 HIS 0.009 0.001 HIS A 822 PHE 0.021 0.002 PHE F 8 TYR 0.022 0.002 TYR D 91 ARG 0.005 0.000 ARG A 569 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3409.64 seconds wall clock time: 63 minutes 54.05 seconds (3834.05 seconds total)