Starting phenix.real_space_refine on Fri Mar 15 09:30:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jx7_36691/03_2024/8jx7_36691.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jx7_36691/03_2024/8jx7_36691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jx7_36691/03_2024/8jx7_36691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jx7_36691/03_2024/8jx7_36691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jx7_36691/03_2024/8jx7_36691.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jx7_36691/03_2024/8jx7_36691.pdb" } resolution = 3.6 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= 0.006 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 7288 2.51 5 N 1858 2.21 5 O 2033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A ASP 750": "OD1" <-> "OD2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1092": "OD1" <-> "OD2" Residue "A GLU 1165": "OE1" <-> "OE2" Residue "A PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1187": "OE1" <-> "OE2" Residue "A PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1263": "OE1" <-> "OE2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A GLU 1274": "OE1" <-> "OE2" Residue "A PHE 1418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1429": "OE1" <-> "OE2" Residue "A GLU 1432": "OE1" <-> "OE2" Residue "A PHE 1483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1508": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11237 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1416, 11237 Classifications: {'peptide': 1416} Link IDs: {'PTRANS': 44, 'TRANS': 1371} Chain breaks: 3 Time building chain proxies: 6.24, per 1000 atoms: 0.56 Number of scatterers: 11237 At special positions: 0 Unit cell: (111.28, 126.26, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2033 8.00 N 1858 7.00 C 7288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 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: 4.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2678 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 70.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 18 removed outlier: 4.167A pdb=" N SER A 18 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 54 removed outlier: 3.580A pdb=" N LEU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Proline residue: A 36 - end of helix removed outlier: 3.528A pdb=" N LEU A 43 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.562A pdb=" N VAL A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 removed outlier: 4.562A pdb=" N VAL A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 4.086A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 129 through 156 removed outlier: 3.708A pdb=" N PHE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 182 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.883A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 234 through 256 removed outlier: 3.842A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.540A pdb=" N ALA A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.727A pdb=" N LYS A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 removed outlier: 3.572A pdb=" N ASN A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.604A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 407 removed outlier: 4.037A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 367 " --> pdb=" O CYS A 363 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 417 through 426 removed outlier: 4.400A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N MET A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.964A pdb=" N ASP A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 442 through 459 Processing helix chain 'A' and resid 462 through 507 removed outlier: 3.875A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.240A pdb=" N LYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 517 through 569 removed outlier: 3.698A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 548 " --> pdb=" O CYS A 544 " (cutoff:3.500A) Proline residue: A 554 - end of helix removed outlier: 4.302A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 596 removed outlier: 3.956A pdb=" N THR A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 597 through 618 removed outlier: 3.793A pdb=" N MET A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 4.299A pdb=" N ILE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 721 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.530A pdb=" N GLU A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 762 through 778 removed outlier: 3.708A pdb=" N ASN A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.624A pdb=" N ASN A 801 " --> pdb=" O LYS A 797 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 802 " --> pdb=" O HIS A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 897 removed outlier: 3.602A pdb=" N GLU A 893 " --> pdb=" O SER A 890 " (cutoff:3.500A) Proline residue: A 895 - end of helix Processing helix chain 'A' and resid 898 through 913 removed outlier: 3.738A pdb=" N THR A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 974 Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.752A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1010 removed outlier: 3.687A pdb=" N ILE A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1067 removed outlier: 3.530A pdb=" N GLN A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A1047 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A1051 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.616A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.774A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1094 Processing helix chain 'A' and resid 1094 through 1101 Processing helix chain 'A' and resid 1102 through 1118 removed outlier: 4.348A pdb=" N GLY A1108 " --> pdb=" O THR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1169 removed outlier: 4.331A pdb=" N ILE A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.783A pdb=" N TYR A1134 " --> pdb=" O LEU A1130 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A1155 " --> pdb=" O LEU A1151 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.616A pdb=" N ASN A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A1200 " --> pdb=" O CYS A1196 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A1201 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1208 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1243 removed outlier: 4.185A pdb=" N PHE A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1266 removed outlier: 3.811A pdb=" N ASN A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1277 Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.741A pdb=" N PHE A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1376 removed outlier: 4.062A pdb=" N LYS A1376 " --> pdb=" O ASP A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1402 through 1413 Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1424 through 1428 removed outlier: 3.576A pdb=" N SER A1427 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 removed outlier: 3.860A pdb=" N LEU A1444 " --> pdb=" O GLY A1440 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A1445 " --> pdb=" O GLN A1441 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS A1446 " --> pdb=" O ARG A1442 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A1447 " --> pdb=" O GLN A1443 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1448 " --> pdb=" O LEU A1444 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1483 Processing helix chain 'A' and resid 1484 through 1486 No H-bonds generated for 'chain 'A' and resid 1484 through 1486' Processing helix chain 'A' and resid 1494 through 1498 removed outlier: 3.902A pdb=" N THR A1497 " --> pdb=" O ARG A1494 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A1498 " --> pdb=" O LEU A1495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1494 through 1498' Processing helix chain 'A' and resid 1517 through 1524 removed outlier: 3.504A pdb=" N GLN A1523 " --> pdb=" O GLU A1519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1524 " --> pdb=" O GLU A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1533 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 5.996A pdb=" N ARG A 628 " --> pdb=" O ILE A 697 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 661 removed outlier: 6.735A pdb=" N ARG A 655 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 657 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 661 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS A 692 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.443A pdb=" N ALA A 702 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASP A 785 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 704 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 666 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL A 832 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 831 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS A 842 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 833 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 713 through 714 Processing sheet with id=AA5, first strand: chain 'A' and resid 1323 through 1324 Processing sheet with id=AA6, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 6.371A pdb=" N THR A1378 " --> pdb=" O VAL A1459 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A1458 " --> pdb=" O ILE A1489 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A1491 " --> pdb=" O LEU A1458 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A1460 " --> pdb=" O ILE A1491 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A1330 " --> pdb=" O THR A1490 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLY A1331 " --> pdb=" O MET A1505 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A1507 " --> pdb=" O GLY A1331 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL A1333 " --> pdb=" O LEU A1507 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A1504 " --> pdb=" O CYS A1515 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N CYS A1515 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1506 " --> pdb=" O ILE A1513 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1812 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: 4.02 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3542 1.34 - 1.46: 2706 1.46 - 1.58: 5130 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 11474 Sorted by residual: bond pdb=" C TRP A1294 " pdb=" N PRO A1295 " ideal model delta sigma weight residual 1.331 1.348 -0.016 7.90e-03 1.60e+04 4.22e+00 bond pdb=" CA LEU A1107 " pdb=" C LEU A1107 " ideal model delta sigma weight residual 1.523 1.499 0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CA ALA A 370 " pdb=" C ALA A 370 " ideal model delta sigma weight residual 1.522 1.503 0.020 1.38e-02 5.25e+03 2.01e+00 bond pdb=" C PHE A 591 " pdb=" N PRO A 592 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.36e-02 5.41e+03 1.55e+00 bond pdb=" CB GLU A 3 " pdb=" CG GLU A 3 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 11469 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.59: 249 106.59 - 113.53: 6451 113.53 - 120.46: 4529 120.46 - 127.40: 4224 127.40 - 134.34: 107 Bond angle restraints: 15560 Sorted by residual: angle pdb=" N ILE A 204 " pdb=" CA ILE A 204 " pdb=" C ILE A 204 " ideal model delta sigma weight residual 112.17 107.51 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N VAL A 392 " pdb=" CA VAL A 392 " pdb=" C VAL A 392 " ideal model delta sigma weight residual 112.96 109.61 3.35 1.00e+00 1.00e+00 1.13e+01 angle pdb=" N GLY A1031 " pdb=" CA GLY A1031 " pdb=" C GLY A1031 " ideal model delta sigma weight residual 115.32 111.10 4.22 1.31e+00 5.83e-01 1.04e+01 angle pdb=" CA LEU A 817 " pdb=" CB LEU A 817 " pdb=" CG LEU A 817 " ideal model delta sigma weight residual 116.30 126.41 -10.11 3.50e+00 8.16e-02 8.35e+00 angle pdb=" C ARG A1156 " pdb=" N SER A1157 " pdb=" CA SER A1157 " ideal model delta sigma weight residual 120.09 123.45 -3.36 1.25e+00 6.40e-01 7.22e+00 ... (remaining 15555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5844 17.66 - 35.32: 762 35.32 - 52.98: 191 52.98 - 70.64: 25 70.64 - 88.30: 20 Dihedral angle restraints: 6842 sinusoidal: 2713 harmonic: 4129 Sorted by residual: dihedral pdb=" CA PHE A 824 " pdb=" C PHE A 824 " pdb=" N LEU A 825 " pdb=" CA LEU A 825 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA MET A 438 " pdb=" C MET A 438 " pdb=" N HIS A 439 " pdb=" CA HIS A 439 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG A 655 " pdb=" C ARG A 655 " pdb=" N ASP A 656 " pdb=" CA ASP A 656 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1285 0.039 - 0.077: 436 0.077 - 0.116: 95 0.116 - 0.155: 6 0.155 - 0.193: 2 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA ASP A1092 " pdb=" N ASP A1092 " pdb=" C ASP A1092 " pdb=" CB ASP A1092 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA THR A 553 " pdb=" N THR A 553 " pdb=" C THR A 553 " pdb=" CB THR A 553 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLU A 518 " pdb=" N GLU A 518 " pdb=" C GLU A 518 " pdb=" CB GLU A 518 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1821 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 103 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 104 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 219 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 220 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1418 " -0.011 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE A1418 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A1418 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A1418 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A1418 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1418 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A1418 " 0.000 2.00e-02 2.50e+03 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 125 2.63 - 3.19: 10703 3.19 - 3.76: 17761 3.76 - 4.33: 23541 4.33 - 4.90: 37743 Nonbonded interactions: 89873 Sorted by model distance: nonbonded pdb=" O LEU A 431 " pdb=" OG1 THR A 435 " model vdw 2.057 2.440 nonbonded pdb=" O VAL A 559 " pdb=" OG SER A 563 " model vdw 2.201 2.440 nonbonded pdb=" O ALA A 98 " pdb=" OG1 THR A 102 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP A 22 " pdb=" NE2 GLN A 148 " model vdw 2.224 2.520 nonbonded pdb=" ND2 ASN A 409 " pdb=" O GLU A 687 " model vdw 2.230 2.520 ... (remaining 89868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.850 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.390 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11474 Z= 0.183 Angle : 0.646 10.113 15560 Z= 0.355 Chirality : 0.039 0.193 1824 Planarity : 0.004 0.064 1932 Dihedral : 17.214 88.304 4161 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 27.99 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1408 helix: 0.40 (0.18), residues: 836 sheet: 0.95 (0.62), residues: 72 loop : -0.22 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1200 HIS 0.005 0.001 HIS A1371 PHE 0.035 0.001 PHE A1418 TYR 0.005 0.001 TYR A 206 ARG 0.005 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.8797 (tt) cc_final: 0.8456 (tt) REVERT: A 373 ILE cc_start: 0.8578 (mm) cc_final: 0.8217 (mm) REVERT: A 485 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8550 (mmmm) REVERT: A 551 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8142 (tm-30) REVERT: A 599 MET cc_start: 0.8246 (mmm) cc_final: 0.7892 (mmm) REVERT: A 822 MET cc_start: 0.5305 (mpp) cc_final: 0.4993 (mtt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2098 time to fit residues: 86.7496 Evaluate side-chains 154 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 HIS ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1394 ASN ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11474 Z= 0.381 Angle : 0.804 10.834 15560 Z= 0.413 Chirality : 0.045 0.244 1824 Planarity : 0.005 0.060 1932 Dihedral : 3.992 20.873 1510 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.46 % Allowed : 24.48 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1408 helix: 0.39 (0.17), residues: 880 sheet: 0.29 (0.58), residues: 82 loop : -0.10 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1200 HIS 0.007 0.001 HIS A1371 PHE 0.033 0.002 PHE A 74 TYR 0.023 0.002 TYR A 616 ARG 0.014 0.001 ARG A1289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 166 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 598 MET cc_start: 0.7370 (ppp) cc_final: 0.6523 (ppp) REVERT: A 599 MET cc_start: 0.8261 (mmm) cc_final: 0.8044 (mmm) REVERT: A 1069 MET cc_start: 0.7967 (tpp) cc_final: 0.7321 (tpp) outliers start: 81 outliers final: 41 residues processed: 226 average time/residue: 0.1918 time to fit residues: 66.2118 Evaluate side-chains 193 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1267 VAL Chi-restraints excluded: chain A residue 1274 GLU Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.2980 chunk 39 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 138 optimal weight: 40.0000 chunk 114 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11474 Z= 0.194 Angle : 0.738 13.404 15560 Z= 0.348 Chirality : 0.045 0.292 1824 Planarity : 0.004 0.049 1932 Dihedral : 3.912 19.461 1510 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.94 % Allowed : 25.12 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1408 helix: 0.48 (0.17), residues: 868 sheet: 0.62 (0.61), residues: 72 loop : -0.13 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1200 HIS 0.004 0.001 HIS A1371 PHE 0.024 0.002 PHE A1123 TYR 0.016 0.001 TYR A 885 ARG 0.009 0.001 ARG A 904 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 176 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: A 512 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9233 (mm) REVERT: A 598 MET cc_start: 0.7491 (ppp) cc_final: 0.6618 (ppp) REVERT: A 988 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7243 (ttp) REVERT: A 994 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.7982 (tp) REVERT: A 1073 ASP cc_start: 0.7916 (m-30) cc_final: 0.7595 (m-30) REVERT: A 1531 MET cc_start: 0.9641 (ppp) cc_final: 0.9355 (ppp) outliers start: 62 outliers final: 29 residues processed: 220 average time/residue: 0.2031 time to fit residues: 68.5175 Evaluate side-chains 183 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 136 optimal weight: 40.0000 chunk 67 optimal weight: 0.0870 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 HIS ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11474 Z= 0.186 Angle : 0.740 14.649 15560 Z= 0.341 Chirality : 0.044 0.228 1824 Planarity : 0.004 0.055 1932 Dihedral : 3.880 19.160 1510 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.83 % Allowed : 26.48 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1408 helix: 0.58 (0.17), residues: 869 sheet: 0.71 (0.64), residues: 67 loop : -0.28 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.003 0.000 HIS A1371 PHE 0.032 0.001 PHE A 74 TYR 0.016 0.001 TYR A 970 ARG 0.011 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.215 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 230 ASP cc_start: 0.7440 (p0) cc_final: 0.6928 (p0) REVERT: A 232 GLU cc_start: 0.8049 (mp0) cc_final: 0.7813 (mp0) REVERT: A 440 MET cc_start: 0.7703 (mmm) cc_final: 0.7255 (mmm) REVERT: A 512 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9221 (mm) REVERT: A 599 MET cc_start: 0.7634 (mmm) cc_final: 0.6167 (mmm) REVERT: A 994 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8472 (mm) outliers start: 48 outliers final: 30 residues processed: 201 average time/residue: 0.1832 time to fit residues: 57.3699 Evaluate side-chains 181 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11474 Z= 0.232 Angle : 0.737 12.945 15560 Z= 0.351 Chirality : 0.044 0.286 1824 Planarity : 0.004 0.051 1932 Dihedral : 3.855 19.392 1510 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.86 % Allowed : 27.51 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1408 helix: 0.75 (0.17), residues: 866 sheet: 0.73 (0.65), residues: 67 loop : -0.41 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 309 HIS 0.015 0.001 HIS A1371 PHE 0.013 0.001 PHE A1037 TYR 0.022 0.001 TYR A 885 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 152 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASP cc_start: 0.7603 (p0) cc_final: 0.7396 (p0) REVERT: A 551 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 595 MET cc_start: 0.6946 (ppp) cc_final: 0.5264 (tmm) REVERT: A 600 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7650 (pt) outliers start: 61 outliers final: 39 residues processed: 196 average time/residue: 0.1796 time to fit residues: 54.8592 Evaluate side-chains 177 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11474 Z= 0.191 Angle : 0.779 14.012 15560 Z= 0.358 Chirality : 0.045 0.306 1824 Planarity : 0.004 0.050 1932 Dihedral : 3.894 18.596 1510 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.83 % Allowed : 29.43 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1408 helix: 0.78 (0.17), residues: 864 sheet: 0.79 (0.65), residues: 67 loop : -0.45 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1200 HIS 0.010 0.001 HIS A1371 PHE 0.015 0.001 PHE A1037 TYR 0.025 0.001 TYR A 885 ARG 0.009 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9205 (mm) REVERT: A 551 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 600 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7973 (pt) REVERT: A 688 MET cc_start: 0.7974 (tpp) cc_final: 0.7671 (tpp) outliers start: 48 outliers final: 35 residues processed: 189 average time/residue: 0.1746 time to fit residues: 52.3090 Evaluate side-chains 178 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1243 SER Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1383 ASP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11474 Z= 0.195 Angle : 0.797 12.836 15560 Z= 0.366 Chirality : 0.046 0.329 1824 Planarity : 0.004 0.049 1932 Dihedral : 3.892 18.467 1510 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.07 % Allowed : 29.51 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1408 helix: 0.79 (0.18), residues: 865 sheet: 0.73 (0.64), residues: 68 loop : -0.43 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1200 HIS 0.007 0.001 HIS A1371 PHE 0.013 0.001 PHE A 437 TYR 0.022 0.001 TYR A 616 ARG 0.006 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 LEU cc_start: 0.8821 (pp) cc_final: 0.8501 (pp) REVERT: A 1170 LEU cc_start: 0.9066 (pp) cc_final: 0.8814 (tt) REVERT: A 1270 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8438 (tm-30) outliers start: 51 outliers final: 41 residues processed: 189 average time/residue: 0.1708 time to fit residues: 51.4211 Evaluate side-chains 185 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 605 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1243 SER Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1383 ASP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11474 Z= 0.198 Angle : 0.802 12.282 15560 Z= 0.369 Chirality : 0.046 0.358 1824 Planarity : 0.004 0.100 1932 Dihedral : 3.894 18.284 1510 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.11 % Allowed : 30.06 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1408 helix: 0.71 (0.17), residues: 856 sheet: 0.76 (0.64), residues: 68 loop : -0.39 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1200 HIS 0.007 0.000 HIS A1371 PHE 0.042 0.001 PHE A1123 TYR 0.016 0.001 TYR A 361 ARG 0.008 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: A 440 MET cc_start: 0.7507 (mmm) cc_final: 0.7208 (mmm) REVERT: A 688 MET cc_start: 0.7875 (tpp) cc_final: 0.7559 (tpp) REVERT: A 907 ASN cc_start: 0.8054 (m110) cc_final: 0.7800 (m-40) REVERT: A 1170 LEU cc_start: 0.9085 (pp) cc_final: 0.8794 (tt) REVERT: A 1270 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 39 outliers final: 34 residues processed: 182 average time/residue: 0.1925 time to fit residues: 54.7250 Evaluate side-chains 184 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1243 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1383 ASP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 81 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11474 Z= 0.262 Angle : 0.835 15.874 15560 Z= 0.396 Chirality : 0.047 0.311 1824 Planarity : 0.004 0.063 1932 Dihedral : 3.965 18.435 1510 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.51 % Allowed : 30.30 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1408 helix: 0.66 (0.17), residues: 863 sheet: 0.69 (0.64), residues: 68 loop : -0.36 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 34 HIS 0.009 0.001 HIS A1371 PHE 0.040 0.002 PHE A1123 TYR 0.012 0.001 TYR A 361 ARG 0.008 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 145 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: A 440 MET cc_start: 0.7642 (mmm) cc_final: 0.7332 (mmm) REVERT: A 688 MET cc_start: 0.8127 (tpp) cc_final: 0.7837 (tpp) outliers start: 44 outliers final: 35 residues processed: 178 average time/residue: 0.1841 time to fit residues: 50.8484 Evaluate side-chains 177 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1243 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASN Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 0.0170 chunk 129 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11474 Z= 0.192 Angle : 0.885 15.784 15560 Z= 0.398 Chirality : 0.049 0.449 1824 Planarity : 0.004 0.051 1932 Dihedral : 3.964 19.813 1510 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.39 % Allowed : 31.50 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1408 helix: 0.65 (0.17), residues: 860 sheet: 0.79 (0.64), residues: 68 loop : -0.38 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 34 HIS 0.005 0.000 HIS A1371 PHE 0.019 0.001 PHE A 909 TYR 0.025 0.001 TYR A 616 ARG 0.003 0.000 ARG A1149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: A 440 MET cc_start: 0.7508 (mmm) cc_final: 0.7106 (mmm) REVERT: A 688 MET cc_start: 0.7970 (tpp) cc_final: 0.7675 (tpp) REVERT: A 1115 MET cc_start: 0.7758 (mmp) cc_final: 0.7555 (mmt) outliers start: 30 outliers final: 26 residues processed: 175 average time/residue: 0.1870 time to fit residues: 50.8816 Evaluate side-chains 171 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1346 CYS Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1499 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 98 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.049508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.036127 restraints weight = 67689.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.037293 restraints weight = 38888.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038119 restraints weight = 26835.722| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11474 Z= 0.189 Angle : 0.879 19.669 15560 Z= 0.395 Chirality : 0.049 0.444 1824 Planarity : 0.004 0.052 1932 Dihedral : 3.950 18.893 1510 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.99 % Allowed : 32.06 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1408 helix: 0.66 (0.18), residues: 868 sheet: 0.83 (0.65), residues: 68 loop : -0.41 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 34 HIS 0.005 0.000 HIS A1371 PHE 0.016 0.001 PHE A 909 TYR 0.009 0.001 TYR A 885 ARG 0.007 0.000 ARG A 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.45 seconds wall clock time: 39 minutes 29.79 seconds (2369.79 seconds total)