Starting phenix.real_space_refine on Sun Apr 14 15:33:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sor_40669/04_2024/8sor_40669_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sor_40669/04_2024/8sor_40669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sor_40669/04_2024/8sor_40669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sor_40669/04_2024/8sor_40669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sor_40669/04_2024/8sor_40669_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sor_40669/04_2024/8sor_40669_trim_updated.pdb" } resolution = 3.96 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= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 10196 2.51 5 N 2776 2.21 5 O 2988 1.98 5 H 16046 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 5": "OE1" <-> "OE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1003": "OD1" <-> "OD2" Residue "A TYR 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1091": "OD1" <-> "OD2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1150": "OD1" <-> "OD2" Residue "A TYR 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1296": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32094 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4237 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 13, 'TRANS': 248} Chain breaks: 2 Chain: "C" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4385 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Chain: "D" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4943 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 5, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 18529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 18529 Unusual residues: {'ADP': 1} Classifications: {'peptide': 1156, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1102, None: 1} Not linked: pdbres="LYS A1358 " pdbres="ADP A1401 " Chain breaks: 6 Time building chain proxies: 13.39, per 1000 atoms: 0.42 Number of scatterers: 32094 At special positions: 0 Unit cell: (91.43, 157.215, 218.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 2 15.00 O 2988 8.00 N 2776 7.00 C 10196 6.00 H 16046 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 335 " distance=2.05 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: 25.38 Conformation dependent library (CDL) restraints added in 3.2 seconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 16 sheets defined 48.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.74 Creating SS restraints... Processing helix chain 'B' and resid 12 through 15 No H-bonds generated for 'chain 'B' and resid 12 through 15' Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 171 through 183 Processing helix chain 'B' and resid 191 through 211 removed outlier: 3.543A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 102 through 204 removed outlier: 3.710A pdb=" N ASP C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 280 removed outlier: 3.539A pdb=" N TYR C 280 " --> pdb=" O SER C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 299 through 321 Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 341 through 362 removed outlier: 3.726A pdb=" N THR C 345 " --> pdb=" O LYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'D' and resid 138 through 265 removed outlier: 3.699A pdb=" N GLN D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 300 through 321 Processing helix chain 'D' and resid 364 through 384 Processing helix chain 'D' and resid 422 through 448 Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 65 through 80 removed outlier: 4.942A pdb=" N SER A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.666A pdb=" N SER A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 237 through 253 removed outlier: 3.913A pdb=" N ILE A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 339 through 357 removed outlier: 4.995A pdb=" N GLY A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.581A pdb=" N CYS A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.641A pdb=" N ASN A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.133A pdb=" N LEU A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 463 through 472 removed outlier: 4.755A pdb=" N HIS A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLN A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 503 removed outlier: 4.778A pdb=" N ALA A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 546 removed outlier: 3.622A pdb=" N SER A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 558 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 570 through 581 removed outlier: 4.410A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 608 removed outlier: 4.897A pdb=" N VAL A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 625 removed outlier: 4.579A pdb=" N SER A 614 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 617 " --> pdb=" O SER A 614 " (cutoff:3.500A) Proline residue: A 618 - end of helix removed outlier: 3.690A pdb=" N GLY A 623 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.625A pdb=" N TYR A 654 " --> pdb=" O LYS A 650 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Proline residue: A 662 - end of helix removed outlier: 4.918A pdb=" N CYS A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 684 Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 696 through 699 No H-bonds generated for 'chain 'A' and resid 696 through 699' Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 726 through 733 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 765 through 776 Processing helix chain 'A' and resid 781 through 789 Processing helix chain 'A' and resid 791 through 806 Processing helix chain 'A' and resid 821 through 824 No H-bonds generated for 'chain 'A' and resid 821 through 824' Processing helix chain 'A' and resid 939 through 965 Processing helix chain 'A' and resid 1022 through 1025 No H-bonds generated for 'chain 'A' and resid 1022 through 1025' Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1270 through 1275 Proline residue: A1273 - end of helix No H-bonds generated for 'chain 'A' and resid 1270 through 1275' Processing sheet with id= A, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.029A pdb=" N GLY B 232 " --> pdb=" O ILE B 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 89 through 92 removed outlier: 3.921A pdb=" N GLY B 139 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 64 removed outlier: 3.591A pdb=" N GLY B 123 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 112 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.796A pdb=" N SER C 260 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 329 through 331 Processing sheet with id= F, first strand: chain 'D' and resid 394 through 397 removed outlier: 3.528A pdb=" N LYS D 402 " --> pdb=" O ASP D 397 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 39 through 45 removed outlier: 3.796A pdb=" N LYS A 89 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 154 through 156 Processing sheet with id= I, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.634A pdb=" N ILE A1019 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A1011 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 998 " --> pdb=" O CYS A1011 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1086 through 1089 removed outlier: 3.517A pdb=" N GLN A1086 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A1047 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1121 through 1125 removed outlier: 3.541A pdb=" N TRP A1124 " --> pdb=" O LEU A1112 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A1111 " --> pdb=" O PHE A1104 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A1100 " --> pdb=" O ALA A1115 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1167 through 1169 removed outlier: 3.529A pdb=" N TRP A1168 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1199 through 1203 removed outlier: 3.541A pdb=" N SER A1211 " --> pdb=" O ALA A1202 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A1222 " --> pdb=" O MET A1212 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP A1214 " --> pdb=" O ARG A1220 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG A1220 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1266 through 1269 Processing sheet with id= O, first strand: chain 'A' and resid 1289 through 1295 Processing sheet with id= P, first strand: chain 'A' and resid 985 through 988 removed outlier: 6.379A pdb=" N VAL A1356 " --> pdb=" O VAL A 986 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A 988 " --> pdb=" O VAL A1354 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A1354 " --> pdb=" O HIS A 988 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A1348 " --> pdb=" O ASP A1334 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A1334 " --> pdb=" O ALA A1348 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 2232 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: 13.45 Time building geometry restraints manager: 26.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16008 1.03 - 1.23: 62 1.23 - 1.42: 6780 1.42 - 1.62: 9444 1.62 - 1.81: 132 Bond restraints: 32426 Sorted by residual: bond pdb=" N CYS D 137 " pdb=" CA CYS D 137 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" C4 ADP A1401 " pdb=" C5 ADP A1401 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" N CYS D 137 " pdb=" H CYS D 137 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C5 ADP A1401 " pdb=" C6 ADP A1401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CA TYR D 333 " pdb=" C TYR D 333 " ideal model delta sigma weight residual 1.524 1.501 0.023 2.25e-02 1.98e+03 1.03e+00 ... (remaining 32421 not shown) Histogram of bond angle deviations from ideal: 73.60 - 86.09: 6 86.09 - 98.59: 0 98.59 - 111.09: 35873 111.09 - 123.58: 20068 123.58 - 136.08: 2702 Bond angle restraints: 58649 Sorted by residual: angle pdb=" C PHE D 390 " pdb=" CA PHE D 390 " pdb=" HA PHE D 390 " ideal model delta sigma weight residual 109.00 73.60 35.40 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C SER B 212 " pdb=" CA SER B 212 " pdb=" HA SER B 212 " ideal model delta sigma weight residual 109.00 74.16 34.84 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CB PHE D 390 " pdb=" CA PHE D 390 " pdb=" HA PHE D 390 " ideal model delta sigma weight residual 109.00 74.33 34.67 3.00e+00 1.11e-01 1.34e+02 angle pdb=" CB SER B 212 " pdb=" CA SER B 212 " pdb=" HA SER B 212 " ideal model delta sigma weight residual 109.00 74.94 34.06 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N SER B 212 " pdb=" CA SER B 212 " pdb=" HA SER B 212 " ideal model delta sigma weight residual 110.00 76.05 33.95 3.00e+00 1.11e-01 1.28e+02 ... (remaining 58644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13674 17.56 - 35.13: 1118 35.13 - 52.69: 300 52.69 - 70.26: 79 70.26 - 87.82: 14 Dihedral angle restraints: 15185 sinusoidal: 8322 harmonic: 6863 Sorted by residual: dihedral pdb=" CB CYS C 308 " pdb=" SG CYS C 308 " pdb=" SG CYS C 335 " pdb=" CB CYS C 335 " ideal model delta sinusoidal sigma weight residual 93.00 159.05 -66.05 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CA PHE A 259 " pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA HIS A 988 " pdb=" C HIS A 988 " pdb=" N LEU A 989 " pdb=" CA LEU A 989 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 15182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2278 0.075 - 0.150: 175 0.150 - 0.226: 0 0.226 - 0.301: 0 0.301 - 0.376: 2 Chirality restraints: 2455 Sorted by residual: chirality pdb=" CA SER B 212 " pdb=" N SER B 212 " pdb=" C SER B 212 " pdb=" CB SER B 212 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA PHE D 390 " pdb=" N PHE D 390 " pdb=" C PHE D 390 " pdb=" CB PHE D 390 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ILE D 276 " pdb=" N ILE D 276 " pdb=" C ILE D 276 " pdb=" CB ILE D 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 2452 not shown) Planarity restraints: 4718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1083 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A1084 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1084 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1084 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 661 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 662 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 62 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 63 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " 0.020 5.00e-02 4.00e+02 ... (remaining 4715 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 568 2.07 - 2.70: 53358 2.70 - 3.34: 96943 3.34 - 3.97: 119234 3.97 - 4.60: 192000 Nonbonded interactions: 462103 Sorted by model distance: nonbonded pdb=" OE1 GLN A1305 " pdb=" H GLN A1305 " model vdw 1.438 1.850 nonbonded pdb=" OE1 GLN D 281 " pdb=" H GLN D 281 " model vdw 1.502 1.850 nonbonded pdb=" O ALA A 238 " pdb="HH11 ARG A 301 " model vdw 1.532 1.850 nonbonded pdb=" HE1 TRP B 146 " pdb=" O PRO B 160 " model vdw 1.539 1.850 nonbonded pdb="HD22 ASN A 997 " pdb=" OD1 ASN A1013 " model vdw 1.541 1.850 ... (remaining 462098 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: 2.360 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: 0.470 Extract box with map and model: 11.800 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 102.120 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.004 0.036 16380 Z= 0.252 Angle : 0.615 7.097 22136 Z= 0.343 Chirality : 0.040 0.376 2455 Planarity : 0.003 0.039 2826 Dihedral : 14.389 87.823 6168 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 7.72 % Favored : 92.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.27 % 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: -0.05 (0.19), residues: 1956 helix: 1.15 (0.17), residues: 951 sheet: -1.44 (0.32), residues: 243 loop : -0.99 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.008 0.001 HIS B 271 PHE 0.014 0.001 PHE A 38 TYR 0.015 0.002 TYR A 702 ARG 0.004 0.000 ARG A1292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.6626 time to fit residues: 153.6165 Evaluate side-chains 149 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain A residue 355 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.0360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16380 Z= 0.322 Angle : 0.581 6.441 22136 Z= 0.309 Chirality : 0.042 0.368 2455 Planarity : 0.004 0.043 2826 Dihedral : 5.568 53.923 2160 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 0.79 % Allowed : 8.00 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.04 (0.19), residues: 1956 helix: 1.30 (0.17), residues: 943 sheet: -1.64 (0.32), residues: 242 loop : -1.11 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 111 HIS 0.005 0.001 HIS B 271 PHE 0.016 0.002 PHE A1008 TYR 0.016 0.002 TYR A 702 ARG 0.004 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 165 average time/residue: 0.7137 time to fit residues: 173.9394 Evaluate side-chains 163 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 394 TYR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16380 Z= 0.241 Angle : 0.542 6.066 22136 Z= 0.284 Chirality : 0.040 0.365 2455 Planarity : 0.003 0.041 2826 Dihedral : 5.283 53.493 2155 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 1.01 % Allowed : 8.40 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.12 (0.19), residues: 1956 helix: 1.50 (0.17), residues: 943 sheet: -1.64 (0.32), residues: 248 loop : -1.08 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 111 HIS 0.010 0.001 HIS C 388 PHE 0.016 0.001 PHE A1008 TYR 0.016 0.001 TYR D 338 ARG 0.002 0.000 ARG A1292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5532 (mm-30) REVERT: A 1025 MET cc_start: 0.7411 (mmt) cc_final: 0.7156 (mmt) outliers start: 18 outliers final: 13 residues processed: 175 average time/residue: 0.7001 time to fit residues: 184.1509 Evaluate side-chains 167 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain D residue 394 TYR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16380 Z= 0.351 Angle : 0.581 6.055 22136 Z= 0.307 Chirality : 0.042 0.367 2455 Planarity : 0.004 0.046 2826 Dihedral : 5.292 52.421 2155 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 1.52 % Allowed : 8.57 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1956 helix: 1.34 (0.17), residues: 946 sheet: -1.84 (0.32), residues: 248 loop : -1.26 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 111 HIS 0.006 0.001 HIS A1005 PHE 0.018 0.002 PHE A1008 TYR 0.016 0.002 TYR A 702 ARG 0.003 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5600 (mm-30) REVERT: A 1025 MET cc_start: 0.7457 (mmt) cc_final: 0.7242 (mmt) outliers start: 27 outliers final: 20 residues processed: 178 average time/residue: 0.6389 time to fit residues: 172.7238 Evaluate side-chains 175 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 330 CYS Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16380 Z= 0.289 Angle : 0.557 7.711 22136 Z= 0.292 Chirality : 0.041 0.367 2455 Planarity : 0.004 0.043 2826 Dihedral : 5.225 52.787 2155 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.76 % Rotamer: Outliers : 1.35 % Allowed : 9.30 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.06 (0.19), residues: 1956 helix: 1.43 (0.17), residues: 945 sheet: -1.85 (0.31), residues: 246 loop : -1.25 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.005 0.001 HIS A1005 PHE 0.017 0.001 PHE A1008 TYR 0.015 0.002 TYR A 702 ARG 0.003 0.000 ARG A1292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5533 (mm-30) REVERT: A 1025 MET cc_start: 0.7429 (mmt) cc_final: 0.7225 (mmt) outliers start: 24 outliers final: 20 residues processed: 173 average time/residue: 0.6847 time to fit residues: 176.6167 Evaluate side-chains 175 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1005 HIS A1131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16380 Z= 0.170 Angle : 0.512 6.449 22136 Z= 0.264 Chirality : 0.039 0.365 2455 Planarity : 0.003 0.042 2826 Dihedral : 4.965 50.096 2155 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 1.35 % Allowed : 9.70 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.33 (0.19), residues: 1956 helix: 1.73 (0.17), residues: 945 sheet: -1.70 (0.32), residues: 246 loop : -1.02 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 442 HIS 0.005 0.001 HIS A1005 PHE 0.013 0.001 PHE A1008 TYR 0.012 0.001 TYR A 702 ARG 0.003 0.000 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1025 MET cc_start: 0.7508 (mmt) cc_final: 0.7258 (mmt) outliers start: 24 outliers final: 22 residues processed: 179 average time/residue: 0.7245 time to fit residues: 198.1778 Evaluate side-chains 178 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 446 GLN A 777 GLN A1131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16380 Z= 0.182 Angle : 0.503 6.364 22136 Z= 0.259 Chirality : 0.039 0.364 2455 Planarity : 0.003 0.040 2826 Dihedral : 4.768 45.746 2155 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 1.35 % Allowed : 9.81 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.53 (0.20), residues: 1956 helix: 1.91 (0.17), residues: 945 sheet: -1.60 (0.32), residues: 246 loop : -0.94 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.003 0.001 HIS A 988 PHE 0.012 0.001 PHE A1008 TYR 0.013 0.001 TYR A 702 ARG 0.002 0.000 ARG A1292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1025 MET cc_start: 0.7495 (mmt) cc_final: 0.7210 (mmt) outliers start: 24 outliers final: 18 residues processed: 178 average time/residue: 0.6510 time to fit residues: 174.6920 Evaluate side-chains 175 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 chunk 149 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16380 Z= 0.203 Angle : 0.510 7.692 22136 Z= 0.263 Chirality : 0.039 0.365 2455 Planarity : 0.003 0.041 2826 Dihedral : 4.734 45.169 2155 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 1.41 % Allowed : 9.81 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.56 (0.20), residues: 1956 helix: 1.92 (0.17), residues: 945 sheet: -1.56 (0.33), residues: 246 loop : -0.93 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.006 0.001 HIS C 388 PHE 0.013 0.001 PHE A1008 TYR 0.012 0.001 TYR A 702 ARG 0.002 0.000 ARG A1292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 1025 MET cc_start: 0.7502 (mmt) cc_final: 0.7217 (mmt) REVERT: A 1036 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7644 (mp) outliers start: 25 outliers final: 20 residues processed: 182 average time/residue: 0.6643 time to fit residues: 183.7267 Evaluate side-chains 181 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16380 Z= 0.286 Angle : 0.543 8.140 22136 Z= 0.282 Chirality : 0.040 0.368 2455 Planarity : 0.004 0.041 2826 Dihedral : 4.846 46.720 2155 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 1.30 % Allowed : 10.20 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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 (0.19), residues: 1956 helix: 1.80 (0.17), residues: 946 sheet: -1.69 (0.33), residues: 246 loop : -1.01 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.004 0.001 HIS C 388 PHE 0.016 0.001 PHE A1008 TYR 0.014 0.001 TYR A 702 ARG 0.002 0.000 ARG A1171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 442 TRP cc_start: 0.7375 (t60) cc_final: 0.7032 (t60) REVERT: A 1025 MET cc_start: 0.7515 (mmt) cc_final: 0.7228 (mmt) REVERT: A 1036 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7818 (mp) outliers start: 23 outliers final: 21 residues processed: 178 average time/residue: 0.6539 time to fit residues: 176.6859 Evaluate side-chains 178 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16380 Z= 0.221 Angle : 0.525 7.939 22136 Z= 0.270 Chirality : 0.040 0.366 2455 Planarity : 0.003 0.041 2826 Dihedral : 4.805 46.785 2155 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 1.24 % Allowed : 10.37 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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 (0.19), residues: 1956 helix: 1.88 (0.17), residues: 945 sheet: -1.63 (0.33), residues: 246 loop : -0.99 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.004 0.001 HIS C 388 PHE 0.014 0.001 PHE A1008 TYR 0.013 0.001 TYR A 702 ARG 0.005 0.000 ARG A1266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 442 TRP cc_start: 0.7312 (t60) cc_final: 0.7004 (t60) REVERT: A 1025 MET cc_start: 0.7501 (mmt) cc_final: 0.7219 (mmt) REVERT: A 1036 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7785 (mp) outliers start: 22 outliers final: 20 residues processed: 179 average time/residue: 0.6294 time to fit residues: 171.3069 Evaluate side-chains 179 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1258 THR Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1349 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098518 restraints weight = 88183.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098367 restraints weight = 103997.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099142 restraints weight = 93573.393| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16380 Z= 0.185 Angle : 0.513 7.901 22136 Z= 0.262 Chirality : 0.039 0.365 2455 Planarity : 0.003 0.040 2826 Dihedral : 4.724 45.164 2155 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 1.13 % Allowed : 10.65 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.61 (0.20), residues: 1956 helix: 2.00 (0.17), residues: 945 sheet: -1.59 (0.33), residues: 246 loop : -0.92 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.003 0.001 HIS A 988 PHE 0.015 0.001 PHE A1008 TYR 0.013 0.001 TYR A1196 ARG 0.004 0.000 ARG A1266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5843.02 seconds wall clock time: 105 minutes 34.31 seconds (6334.31 seconds total)