Starting phenix.real_space_refine on Mon Nov 18 19:13:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/11_2024/8fod_29346.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/11_2024/8fod_29346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/11_2024/8fod_29346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/11_2024/8fod_29346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/11_2024/8fod_29346.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fod_29346/11_2024/8fod_29346.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 79 5.16 5 C 11110 2.51 5 N 2971 2.21 5 O 3325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17489 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 7607 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7552 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 50, 'TRANS': 932} Chain breaks: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 983, 7552 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 50, 'TRANS': 932} Chain breaks: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 7626 Chain: "A" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3052 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 359} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3507 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3484 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 433, 3484 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 3532 Chain: "C" Number of atoms: 3315 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 428, 3291 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 428, 3291 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 3339 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12831 SG CYS B 336 35.046 94.020 79.568 1.00 12.48 S ATOM 13601 SG CYS B 434 35.839 88.518 76.597 1.00 8.05 S ATOM 13475 SG CYS B 417 40.736 91.345 79.050 1.00 4.95 S ATOM 13912 SG CYS B 474 38.847 93.635 73.896 1.00 3.46 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASN 1 745 " occ=0.31 ... (14 atoms not shown) pdb=" ND2BASN 1 745 " occ=0.69 residue: pdb=" N AGLN 1 941 " occ=0.41 ... (16 atoms not shown) pdb=" NE2BGLN 1 941 " occ=0.59 residue: pdb=" N AHIS 11044 " occ=0.39 ... (18 atoms not shown) pdb=" NE2BHIS 11044 " occ=0.61 residue: pdb=" N AASP 11414 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.55 residue: pdb=" N AASP C 263 " occ=0.93 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.07 residue: pdb=" N ACYS C 399 " occ=0.28 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.72 Time building chain proxies: 17.79, per 1000 atoms: 1.02 Number of scatterers: 17489 At special positions: 0 Unit cell: (114.264, 130.824, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 79 16.00 O 3325 8.00 N 2971 7.00 C 11110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.73 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " Number of angles added : 12 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 50.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain '1' and resid 402 through 419 removed outlier: 3.590A pdb=" N ILE 1 411 " --> pdb=" O HIS 1 407 " (cutoff:3.500A) Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 521 through 523 No H-bonds generated for 'chain '1' and resid 521 through 523' Processing helix chain '1' and resid 597 through 606 Processing helix chain '1' and resid 615 through 631 Processing helix chain '1' and resid 643 through 656 Processing helix chain '1' and resid 659 through 664 Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 701 through 707 Processing helix chain '1' and resid 715 through 725 Processing helix chain '1' and resid 737 through 742 removed outlier: 3.602A pdb=" N ASN 1 742 " --> pdb=" O GLN 1 739 " (cutoff:3.500A) Processing helix chain '1' and resid 743 through 768 removed outlier: 3.572A pdb=" N MET 1 747 " --> pdb=" O ASP 1 743 " (cutoff:3.500A) Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 790 removed outlier: 3.543A pdb=" N THR 1 788 " --> pdb=" O ALA 1 784 " (cutoff:3.500A) Processing helix chain '1' and resid 792 through 807 removed outlier: 4.358A pdb=" N ARG 1 796 " --> pdb=" O THR 1 792 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU 1 801 " --> pdb=" O ASN 1 797 " (cutoff:3.500A) Processing helix chain '1' and resid 868 through 876 Processing helix chain '1' and resid 905 through 927 removed outlier: 3.642A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 929 through 950 Processing helix chain '1' and resid 951 through 954 Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1027 Processing helix chain '1' and resid 1079 through 1094 Processing helix chain '1' and resid 1100 through 1120 Processing helix chain '1' and resid 1123 through 1128 Processing helix chain '1' and resid 1136 through 1140 removed outlier: 3.913A pdb=" N TYR 11140 " --> pdb=" O PRO 11137 " (cutoff:3.500A) Processing helix chain '1' and resid 1146 through 1156 removed outlier: 3.953A pdb=" N GLN 11150 " --> pdb=" O MET 11146 " (cutoff:3.500A) Processing helix chain '1' and resid 1196 through 1201 removed outlier: 3.571A pdb=" N ILE 11201 " --> pdb=" O ASN 11197 " (cutoff:3.500A) Processing helix chain '1' and resid 1202 through 1205 Processing helix chain '1' and resid 1209 through 1216 removed outlier: 3.614A pdb=" N TYR 11213 " --> pdb=" O ASP 11209 " (cutoff:3.500A) Processing helix chain '1' and resid 1218 through 1226 removed outlier: 3.634A pdb=" N VAL 11222 " --> pdb=" O ILE 11218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 11224 " --> pdb=" O ALA 11220 " (cutoff:3.500A) Processing helix chain '1' and resid 1275 through 1280 removed outlier: 4.522A pdb=" N ASP 11279 " --> pdb=" O ARG 11276 " (cutoff:3.500A) Processing helix chain '1' and resid 1322 through 1344 removed outlier: 4.064A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY 11344 " --> pdb=" O LEU 11340 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1395 Processing helix chain '1' and resid 1397 through 1403 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 4.109A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 96 removed outlier: 4.974A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 4.037A pdb=" N ASP A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 118 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 removed outlier: 4.200A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.582A pdb=" N ALA A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 210 through 229 Proline residue: A 222 - end of helix removed outlier: 4.169A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.872A pdb=" N GLU A 236 " --> pdb=" O ASN A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.711A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.852A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.654A pdb=" N LYS A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 371 through 391 removed outlier: 4.553A pdb=" N PHE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 71 through 95 Processing helix chain 'B' and resid 98 through 113 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 120 through 138 removed outlier: 3.570A pdb=" N ARG B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 191 through 208 removed outlier: 4.920A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.882A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 278 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 334 through 348 Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 454 through 468 removed outlier: 3.885A pdb=" N GLY B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'C' and resid 254 through 277 removed outlier: 4.011A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 460 through 469 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 548 through 554 Processing helix chain 'C' and resid 555 through 567 Processing helix chain 'C' and resid 613 through 617 Processing helix chain 'C' and resid 622 through 626 Processing helix chain 'C' and resid 693 through 697 Processing sheet with id=AA1, first strand: chain '1' and resid 515 through 519 removed outlier: 7.131A pdb=" N SER 1 381 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL 1 517 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N MET 1 383 " --> pdb=" O VAL 1 517 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL 1 519 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 519 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP 1 358 " --> pdb=" O PHE 1 369 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS 1 371 " --> pdb=" O TRP 1 356 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TRP 1 356 " --> pdb=" O LYS 1 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 425 through 431 removed outlier: 7.688A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE 1 395 " --> pdb=" O LEU 1 446 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 609 through 612 removed outlier: 6.778A pdb=" N LEU 1 582 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 1 544 " --> pdb=" O SER 1 558 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER 1 542 " --> pdb=" O THR 1 560 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN 1 566 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU 1 536 " --> pdb=" O ASN 1 566 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG 1 537 " --> pdb=" O VAL 1 634 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE 1 636 " --> pdb=" O ARG 1 537 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU 1 539 " --> pdb=" O ILE 1 636 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE 1 635 " --> pdb=" O CYS 1 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 854 through 856 removed outlier: 6.327A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 854 through 856 removed outlier: 6.563A pdb=" N PHE 11038 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL 11054 " --> pdb=" O PHE 11038 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS 11040 " --> pdb=" O LEU 11052 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS 11048 " --> pdb=" O AHIS 11044 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 1129 through 1132 Processing sheet with id=AA7, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.559A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id=AA9, first strand: chain '1' and resid 1356 through 1357 Processing sheet with id=AB1, first strand: chain 'A' and resid 56 through 60 removed outlier: 5.775A pdb=" N ARG A 58 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET A 49 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 85 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 56 through 60 removed outlier: 5.775A pdb=" N ARG A 58 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET A 49 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 325 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AB4, first strand: chain 'B' and resid 181 through 182 removed outlier: 3.775A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 302 removed outlier: 3.890A pdb=" N VAL C 301 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU C 316 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 330 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 377 removed outlier: 4.240A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 681 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 515 through 517 removed outlier: 6.716A pdb=" N LYS C 394 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 430 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE C 396 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE C 432 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 398 " --> pdb=" O PHE C 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.632A pdb=" N TYR C 530 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE C 632 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY C 532 " --> pdb=" O ILE C 632 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET C 631 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 578 through 579 889 hydrogen bonds defined for protein. 2508 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: 7.28 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 7227 1.39 - 1.61: 10531 1.61 - 1.84: 103 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 17873 Sorted by residual: bond pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 1.473 1.579 -0.106 1.40e-02 5.10e+03 5.73e+01 bond pdb=" CD GLN 1 544 " pdb=" NE2 GLN 1 544 " ideal model delta sigma weight residual 1.328 1.192 0.136 2.10e-02 2.27e+03 4.19e+01 bond pdb=" CA ALA 1 649 " pdb=" CB ALA 1 649 " ideal model delta sigma weight residual 1.528 1.463 0.065 1.56e-02 4.11e+03 1.74e+01 bond pdb=" C HIS A 210 " pdb=" O HIS A 210 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.36e-02 5.41e+03 1.39e+01 bond pdb=" CA PRO A 247 " pdb=" C PRO A 247 " ideal model delta sigma weight residual 1.520 1.571 -0.052 1.42e-02 4.96e+03 1.34e+01 ... (remaining 17868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.78: 24254 5.78 - 11.55: 25 11.55 - 17.33: 3 17.33 - 23.11: 1 23.11 - 28.88: 1 Bond angle restraints: 24284 Sorted by residual: angle pdb=" CA PRO A 247 " pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 112.00 83.12 28.88 1.40e+00 5.10e-01 4.26e+02 angle pdb=" CA HIS A 210 " pdb=" C HIS A 210 " pdb=" O HIS A 210 " ideal model delta sigma weight residual 119.80 114.12 5.68 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA HIS A 210 " pdb=" C HIS A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 118.85 123.89 -5.04 9.50e-01 1.11e+00 2.81e+01 angle pdb=" C LEU A 246 " pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 125.00 145.34 -20.34 4.10e+00 5.95e-02 2.46e+01 angle pdb=" C ILE 11409 " pdb=" CA ILE 11409 " pdb=" CB ILE 11409 " ideal model delta sigma weight residual 112.02 105.87 6.15 1.31e+00 5.83e-01 2.21e+01 ... (remaining 24279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 9817 17.67 - 35.34: 833 35.34 - 53.02: 176 53.02 - 70.69: 33 70.69 - 88.36: 20 Dihedral angle restraints: 10879 sinusoidal: 4251 harmonic: 6628 Sorted by residual: dihedral pdb=" CA LEU A 246 " pdb=" C LEU A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LYS B 393 " pdb=" C LYS B 393 " pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta harmonic sigma weight residual 180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR B 71 " pdb=" C THR B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 10876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2513 0.087 - 0.173: 214 0.173 - 0.260: 5 0.260 - 0.346: 1 0.346 - 0.433: 2 Chirality restraints: 2735 Sorted by residual: chirality pdb=" CA PRO A 211 " pdb=" N PRO A 211 " pdb=" C PRO A 211 " pdb=" CB PRO A 211 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CB VAL C 326 " pdb=" CA VAL C 326 " pdb=" CG1 VAL C 326 " pdb=" CG2 VAL C 326 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE C 632 " pdb=" CA ILE C 632 " pdb=" CG1 ILE C 632 " pdb=" CG2 ILE C 632 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 2732 not shown) Planarity restraints: 3165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " 0.089 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A 247 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 1 462 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO 1 463 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO 1 463 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO 1 463 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 35 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 36 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " -0.048 5.00e-02 4.00e+02 ... (remaining 3162 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 658 2.71 - 3.26: 17743 3.26 - 3.81: 27784 3.81 - 4.35: 34547 4.35 - 4.90: 58904 Nonbonded interactions: 139636 Sorted by model distance: nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 303 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 23 " pdb=" O PRO A 328 " model vdw 2.185 3.040 nonbonded pdb=" O ARG 1 537 " pdb=" N ASP 1 633 " model vdw 2.208 3.120 nonbonded pdb=" OD2 ASP C 541 " pdb=" OH TYR C 571 " model vdw 2.248 3.040 nonbonded pdb=" O THR B 166 " pdb=" OG1 THR B 169 " model vdw 2.257 3.040 ... (remaining 139631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 0.010 Normalize map: mean=0, sd=1: 8.510 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 54.750 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 17873 Z= 0.368 Angle : 0.831 28.882 24284 Z= 0.470 Chirality : 0.048 0.433 2735 Planarity : 0.006 0.111 3165 Dihedral : 14.421 88.359 6575 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 0.27 % Allowed : 11.69 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 (0.18), residues: 2221 helix: 0.67 (0.16), residues: 1022 sheet: -0.20 (0.32), residues: 244 loop : -0.02 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 695 HIS 0.012 0.002 HIS B 131 PHE 0.029 0.003 PHE C 268 TYR 0.025 0.002 TYR A 59 ARG 0.031 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 308 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 449 LEU cc_start: 0.7627 (mp) cc_final: 0.7416 (mp) REVERT: 1 567 ILE cc_start: 0.8432 (mm) cc_final: 0.8135 (mm) REVERT: 1 703 MET cc_start: 0.7040 (tpt) cc_final: 0.6415 (tpt) REVERT: 1 855 LEU cc_start: 0.6916 (tt) cc_final: 0.6689 (tp) REVERT: 1 980 ASN cc_start: 0.5490 (t0) cc_final: 0.5245 (t0) REVERT: 1 1015 ILE cc_start: 0.5503 (mm) cc_final: 0.5087 (tt) REVERT: 1 1436 GLU cc_start: 0.6239 (tt0) cc_final: 0.6004 (tt0) REVERT: 1 1438 MET cc_start: 0.5856 (mmt) cc_final: 0.5210 (mmp) REVERT: A 49 MET cc_start: 0.4492 (mtt) cc_final: 0.4257 (mtm) REVERT: B 96 ASN cc_start: 0.6739 (m-40) cc_final: 0.6181 (m-40) REVERT: B 119 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6895 (tm-30) REVERT: B 224 PHE cc_start: 0.6363 (m-80) cc_final: 0.5975 (m-10) REVERT: B 277 TYR cc_start: 0.5576 (m-80) cc_final: 0.5170 (m-80) REVERT: B 388 MET cc_start: 0.7428 (mmm) cc_final: 0.7044 (mmt) REVERT: B 443 ARG cc_start: 0.6224 (mtp180) cc_final: 0.6011 (mtp180) outliers start: 5 outliers final: 1 residues processed: 311 average time/residue: 0.3197 time to fit residues: 149.3647 Evaluate side-chains 208 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 128 optimal weight: 0.0980 chunk 200 optimal weight: 0.6980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 941 GLN A 11024 ASN 11088 HIS 11194 HIS A 210 HIS A 323 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17873 Z= 0.341 Angle : 0.726 8.956 24284 Z= 0.375 Chirality : 0.048 0.372 2735 Planarity : 0.006 0.071 3165 Dihedral : 5.143 29.390 2421 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.39 % Allowed : 12.43 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.26 (0.17), residues: 2221 helix: 0.88 (0.16), residues: 1015 sheet: -0.38 (0.32), residues: 247 loop : -0.32 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 695 HIS 0.009 0.002 HIS B 131 PHE 0.030 0.003 PHE B 375 TYR 0.021 0.002 TYR 11391 ARG 0.006 0.001 ARG C 699 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: 1 703 MET cc_start: 0.7030 (tpt) cc_final: 0.6312 (tpt) REVERT: 1 1015 ILE cc_start: 0.5462 (mm) cc_final: 0.5217 (tt) REVERT: 1 1100 GLU cc_start: 0.5639 (pm20) cc_final: 0.5076 (pt0) REVERT: 1 1438 MET cc_start: 0.6066 (mmt) cc_final: 0.5226 (mmp) REVERT: A 51 PHE cc_start: 0.4498 (OUTLIER) cc_final: 0.4179 (t80) REVERT: B 119 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7222 (tm-30) REVERT: B 128 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.4174 (m-80) REVERT: B 234 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: B 277 TYR cc_start: 0.5995 (m-80) cc_final: 0.5565 (m-80) REVERT: B 415 TRP cc_start: 0.6819 (OUTLIER) cc_final: 0.6223 (m-10) REVERT: B 451 MET cc_start: 0.7501 (mmm) cc_final: 0.7170 (tpp) REVERT: C 288 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7581 (pt) REVERT: C 392 SER cc_start: 0.4873 (m) cc_final: 0.4440 (p) outliers start: 44 outliers final: 17 residues processed: 257 average time/residue: 0.3004 time to fit residues: 118.0765 Evaluate side-chains 213 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 706 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 199 optimal weight: 0.3980 chunk 68 optimal weight: 20.0000 chunk 161 optimal weight: 0.0970 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN A 60 ASN B 418 HIS C 385 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17873 Z= 0.165 Angle : 0.560 9.433 24284 Z= 0.289 Chirality : 0.042 0.277 2735 Planarity : 0.005 0.064 3165 Dihedral : 4.472 25.567 2421 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.38 % Allowed : 13.71 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.81 (0.18), residues: 2221 helix: 1.44 (0.16), residues: 1018 sheet: -0.50 (0.31), residues: 262 loop : -0.04 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 695 HIS 0.008 0.001 HIS B 131 PHE 0.035 0.001 PHE B 375 TYR 0.024 0.001 TYR A 261 ARG 0.013 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 2.059 Fit side-chains revert: symmetry clash REVERT: 1 703 MET cc_start: 0.6687 (tpt) cc_final: 0.5876 (tpt) REVERT: 1 706 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7467 (m) REVERT: 1 1015 ILE cc_start: 0.5424 (mm) cc_final: 0.5100 (tt) REVERT: 1 1040 LYS cc_start: 0.7261 (mtpp) cc_final: 0.6756 (mtpt) REVERT: 1 1168 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6688 (pt) REVERT: 1 1276 ARG cc_start: 0.5642 (tpt170) cc_final: 0.4939 (tpt170) REVERT: 1 1438 MET cc_start: 0.5928 (mmt) cc_final: 0.4863 (mmm) REVERT: B 121 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 277 TYR cc_start: 0.5870 (m-80) cc_final: 0.5439 (m-80) REVERT: B 451 MET cc_start: 0.7562 (mmm) cc_final: 0.7228 (tpp) REVERT: C 392 SER cc_start: 0.5141 (m) cc_final: 0.4685 (p) outliers start: 25 outliers final: 10 residues processed: 234 average time/residue: 0.2927 time to fit residues: 105.8185 Evaluate side-chains 211 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 706 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.4980 chunk 151 optimal weight: 5.9990 chunk 104 optimal weight: 0.0770 chunk 22 optimal weight: 0.0000 chunk 95 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN A 265 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17873 Z= 0.255 Angle : 0.625 11.303 24284 Z= 0.319 Chirality : 0.045 0.318 2735 Planarity : 0.005 0.060 3165 Dihedral : 4.634 19.449 2419 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 13.18 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.57 (0.18), residues: 2221 helix: 1.32 (0.16), residues: 1018 sheet: -0.53 (0.31), residues: 273 loop : -0.30 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 376 HIS 0.007 0.001 HIS B 131 PHE 0.039 0.002 PHE B 375 TYR 0.014 0.002 TYR C 307 ARG 0.005 0.001 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 1.921 Fit side-chains REVERT: 1 1015 ILE cc_start: 0.5303 (mm) cc_final: 0.4906 (tt) REVERT: 1 1040 LYS cc_start: 0.7231 (mtpp) cc_final: 0.6733 (mtpt) REVERT: 1 1168 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6839 (mt) REVERT: 1 1276 ARG cc_start: 0.5709 (tpt170) cc_final: 0.4928 (tpt170) REVERT: 1 1351 SER cc_start: 0.7652 (m) cc_final: 0.7157 (p) REVERT: 1 1438 MET cc_start: 0.5911 (mmt) cc_final: 0.4869 (mmm) REVERT: A 51 PHE cc_start: 0.4784 (OUTLIER) cc_final: 0.3095 (m-80) REVERT: B 121 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7607 (tt) REVERT: B 128 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.4207 (m-80) REVERT: B 234 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6182 (tt0) REVERT: B 451 MET cc_start: 0.7651 (mmm) cc_final: 0.7321 (tpp) REVERT: C 272 ILE cc_start: 0.6044 (OUTLIER) cc_final: 0.5784 (mm) REVERT: C 392 SER cc_start: 0.5203 (m) cc_final: 0.4741 (p) REVERT: C 480 ILE cc_start: 0.7616 (mt) cc_final: 0.7411 (mp) REVERT: C 537 ASP cc_start: 0.7304 (p0) cc_final: 0.7035 (p0) outliers start: 36 outliers final: 21 residues processed: 234 average time/residue: 0.2872 time to fit residues: 105.7339 Evaluate side-chains 223 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.0170 chunk 121 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 0.0020 chunk 182 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.0230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17873 Z= 0.169 Angle : 0.547 11.398 24284 Z= 0.280 Chirality : 0.042 0.290 2735 Planarity : 0.004 0.060 3165 Dihedral : 4.332 19.538 2419 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.70 % Allowed : 14.72 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.81 (0.18), residues: 2221 helix: 1.56 (0.17), residues: 1019 sheet: -0.57 (0.31), residues: 277 loop : -0.17 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 31 HIS 0.008 0.001 HIS B 131 PHE 0.031 0.001 PHE B 375 TYR 0.016 0.001 TYR B 352 ARG 0.007 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 2.085 Fit side-chains REVERT: 1 685 PHE cc_start: 0.7119 (t80) cc_final: 0.6887 (t80) REVERT: 1 1015 ILE cc_start: 0.5248 (mm) cc_final: 0.4955 (tt) REVERT: 1 1168 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6768 (mt) REVERT: 1 1276 ARG cc_start: 0.5651 (tpt170) cc_final: 0.4880 (tpt170) REVERT: 1 1351 SER cc_start: 0.7778 (m) cc_final: 0.7334 (p) REVERT: 1 1438 MET cc_start: 0.5877 (mmt) cc_final: 0.4817 (mmm) REVERT: A 51 PHE cc_start: 0.4581 (OUTLIER) cc_final: 0.2879 (m-80) REVERT: B 128 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.4130 (m-80) REVERT: B 234 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: B 451 MET cc_start: 0.7700 (mmm) cc_final: 0.7370 (tpp) REVERT: C 392 SER cc_start: 0.5191 (m) cc_final: 0.4735 (p) REVERT: C 480 ILE cc_start: 0.7537 (mt) cc_final: 0.7313 (mp) REVERT: C 537 ASP cc_start: 0.7318 (p0) cc_final: 0.7053 (p0) outliers start: 30 outliers final: 20 residues processed: 229 average time/residue: 0.3277 time to fit residues: 117.4720 Evaluate side-chains 218 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 3.9990 chunk 192 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.0470 chunk 52 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 524 ASN 11024 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17873 Z= 0.148 Angle : 0.526 8.429 24284 Z= 0.267 Chirality : 0.041 0.261 2735 Planarity : 0.004 0.058 3165 Dihedral : 4.117 20.686 2419 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.49 % Allowed : 14.88 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2221 helix: 1.72 (0.16), residues: 1023 sheet: -0.46 (0.31), residues: 275 loop : 0.03 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 31 HIS 0.007 0.001 HIS B 131 PHE 0.034 0.001 PHE B 375 TYR 0.015 0.001 TYR B 352 ARG 0.009 0.000 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 2.216 Fit side-chains REVERT: 1 685 PHE cc_start: 0.7064 (t80) cc_final: 0.6858 (t80) REVERT: 1 1015 ILE cc_start: 0.5546 (mm) cc_final: 0.4968 (tt) REVERT: 1 1168 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6450 (pt) REVERT: 1 1276 ARG cc_start: 0.5460 (tpt170) cc_final: 0.4686 (tpt170) REVERT: 1 1338 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7273 (mm) REVERT: 1 1351 SER cc_start: 0.7946 (m) cc_final: 0.7544 (p) REVERT: 1 1438 MET cc_start: 0.5855 (mmt) cc_final: 0.4891 (mmm) REVERT: A 51 PHE cc_start: 0.4412 (OUTLIER) cc_final: 0.2633 (m-80) REVERT: A 231 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: B 121 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7524 (tt) REVERT: B 128 TYR cc_start: 0.5881 (OUTLIER) cc_final: 0.4038 (m-80) REVERT: B 234 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: B 451 MET cc_start: 0.7695 (mmm) cc_final: 0.7363 (tpp) REVERT: C 272 ILE cc_start: 0.5964 (OUTLIER) cc_final: 0.5719 (mm) REVERT: C 392 SER cc_start: 0.5136 (m) cc_final: 0.4666 (p) REVERT: C 537 ASP cc_start: 0.7355 (p0) cc_final: 0.7075 (p0) outliers start: 26 outliers final: 15 residues processed: 226 average time/residue: 0.3003 time to fit residues: 105.0594 Evaluate side-chains 222 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 524 ASN Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 524 ASN 11024 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17873 Z= 0.217 Angle : 0.569 7.843 24284 Z= 0.290 Chirality : 0.043 0.309 2735 Planarity : 0.005 0.059 3165 Dihedral : 4.294 24.036 2419 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.59 % Allowed : 15.09 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.89 (0.18), residues: 2221 helix: 1.56 (0.16), residues: 1030 sheet: -0.56 (0.31), residues: 278 loop : -0.04 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 376 HIS 0.006 0.001 HIS B 131 PHE 0.036 0.002 PHE B 375 TYR 0.018 0.002 TYR C 530 ARG 0.009 0.001 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 2.024 Fit side-chains REVERT: 1 685 PHE cc_start: 0.7131 (t80) cc_final: 0.6927 (t80) REVERT: 1 1015 ILE cc_start: 0.5392 (mm) cc_final: 0.4867 (tt) REVERT: 1 1168 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6489 (pt) REVERT: 1 1276 ARG cc_start: 0.5737 (tpt170) cc_final: 0.4955 (tpt170) REVERT: 1 1351 SER cc_start: 0.8006 (m) cc_final: 0.7619 (p) REVERT: 1 1438 MET cc_start: 0.5792 (mmt) cc_final: 0.4846 (mmm) REVERT: A 51 PHE cc_start: 0.4408 (OUTLIER) cc_final: 0.2706 (m-80) REVERT: A 231 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: B 121 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7607 (tt) REVERT: B 128 TYR cc_start: 0.6028 (OUTLIER) cc_final: 0.4192 (m-80) REVERT: B 234 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6099 (tt0) REVERT: B 451 MET cc_start: 0.7751 (mmm) cc_final: 0.7431 (tpp) REVERT: C 392 SER cc_start: 0.5212 (m) cc_final: 0.4736 (p) REVERT: C 537 ASP cc_start: 0.7305 (p0) cc_final: 0.7017 (p0) outliers start: 28 outliers final: 20 residues processed: 220 average time/residue: 0.2851 time to fit residues: 99.1598 Evaluate side-chains 222 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1188 SER Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN 11036 ASN 11388 GLN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17873 Z= 0.297 Angle : 0.655 10.512 24284 Z= 0.335 Chirality : 0.045 0.364 2735 Planarity : 0.005 0.063 3165 Dihedral : 4.798 23.719 2419 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.13 % Allowed : 14.61 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.42 (0.18), residues: 2221 helix: 1.25 (0.16), residues: 1021 sheet: -0.89 (0.31), residues: 281 loop : -0.33 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 695 HIS 0.007 0.001 HIS B 131 PHE 0.044 0.002 PHE B 375 TYR 0.019 0.002 TYR C 307 ARG 0.007 0.001 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: 1 1015 ILE cc_start: 0.5362 (mm) cc_final: 0.4888 (tt) REVERT: 1 1168 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6844 (mt) REVERT: 1 1351 SER cc_start: 0.8045 (m) cc_final: 0.7698 (p) REVERT: 1 1438 MET cc_start: 0.5768 (mmt) cc_final: 0.4694 (mmp) REVERT: A 231 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6792 (tm-30) REVERT: B 87 LEU cc_start: 0.7119 (mp) cc_final: 0.6725 (mp) REVERT: B 121 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7669 (tt) REVERT: B 128 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.4375 (m-80) REVERT: B 234 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6118 (tt0) REVERT: B 415 TRP cc_start: 0.6630 (OUTLIER) cc_final: 0.6107 (m-10) REVERT: B 451 MET cc_start: 0.7791 (mmm) cc_final: 0.7515 (tpp) REVERT: C 537 ASP cc_start: 0.7413 (p0) cc_final: 0.7146 (p0) REVERT: C 632 ILE cc_start: 0.7089 (tp) cc_final: 0.6611 (mt) REVERT: C 672 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7839 (p) outliers start: 38 outliers final: 27 residues processed: 236 average time/residue: 0.2874 time to fit residues: 106.2536 Evaluate side-chains 229 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1188 SER Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.0040 chunk 186 optimal weight: 0.7980 chunk 198 optimal weight: 0.0470 chunk 119 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 0.0770 chunk 179 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN B 185 ASN B 418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17873 Z= 0.154 Angle : 0.540 7.561 24284 Z= 0.275 Chirality : 0.042 0.332 2735 Planarity : 0.004 0.058 3165 Dihedral : 4.265 20.471 2419 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.12 % Allowed : 15.67 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.93 (0.18), residues: 2221 helix: 1.59 (0.16), residues: 1036 sheet: -0.46 (0.32), residues: 268 loop : -0.07 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 376 HIS 0.011 0.001 HIS 11194 PHE 0.034 0.001 PHE B 375 TYR 0.019 0.001 TYR B 62 ARG 0.008 0.001 ARG C 654 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 2.059 Fit side-chains REVERT: 1 661 SER cc_start: 0.6665 (OUTLIER) cc_final: 0.6375 (t) REVERT: 1 1015 ILE cc_start: 0.5367 (mm) cc_final: 0.4864 (tt) REVERT: 1 1168 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6588 (pt) REVERT: 1 1276 ARG cc_start: 0.5453 (tpt170) cc_final: 0.4715 (tpp-160) REVERT: 1 1351 SER cc_start: 0.8058 (m) cc_final: 0.7723 (p) REVERT: 1 1438 MET cc_start: 0.5731 (mmt) cc_final: 0.4753 (mmm) REVERT: A 231 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: B 87 LEU cc_start: 0.6822 (mp) cc_final: 0.6553 (mp) REVERT: B 128 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.4036 (m-80) REVERT: B 415 TRP cc_start: 0.6475 (OUTLIER) cc_final: 0.5775 (m-10) REVERT: B 451 MET cc_start: 0.7684 (mmm) cc_final: 0.7428 (tpp) REVERT: C 481 GLN cc_start: 0.6267 (tp-100) cc_final: 0.5876 (tp-100) REVERT: C 537 ASP cc_start: 0.7342 (p0) cc_final: 0.7058 (p0) outliers start: 19 outliers final: 13 residues processed: 219 average time/residue: 0.2801 time to fit residues: 95.8609 Evaluate side-chains 218 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 175 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17873 Z= 0.178 Angle : 0.549 10.535 24284 Z= 0.279 Chirality : 0.043 0.560 2735 Planarity : 0.004 0.059 3165 Dihedral : 4.242 20.765 2419 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.12 % Allowed : 15.67 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.96 (0.18), residues: 2221 helix: 1.62 (0.16), residues: 1036 sheet: -0.47 (0.32), residues: 263 loop : -0.06 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 376 HIS 0.021 0.001 HIS B 418 PHE 0.036 0.002 PHE B 375 TYR 0.015 0.001 TYR B 62 ARG 0.013 0.001 ARG B 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 2.179 Fit side-chains REVERT: 1 446 LEU cc_start: 0.7248 (tp) cc_final: 0.6855 (tt) REVERT: 1 1015 ILE cc_start: 0.5336 (mm) cc_final: 0.4898 (tt) REVERT: 1 1168 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6566 (pt) REVERT: 1 1276 ARG cc_start: 0.5565 (tpt170) cc_final: 0.5168 (tpt170) REVERT: 1 1351 SER cc_start: 0.8095 (m) cc_final: 0.7722 (p) REVERT: 1 1438 MET cc_start: 0.5666 (mmt) cc_final: 0.4684 (mmm) REVERT: A 231 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6790 (tm-30) REVERT: B 87 LEU cc_start: 0.6882 (mp) cc_final: 0.6574 (mp) REVERT: B 128 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.4129 (m-80) REVERT: B 234 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: B 341 MET cc_start: 0.5220 (ptp) cc_final: 0.4882 (ptp) REVERT: B 451 MET cc_start: 0.7686 (mmm) cc_final: 0.7435 (tpp) REVERT: C 481 GLN cc_start: 0.6210 (tp-100) cc_final: 0.5957 (tp40) REVERT: C 537 ASP cc_start: 0.7347 (p0) cc_final: 0.7102 (p0) outliers start: 19 outliers final: 12 residues processed: 215 average time/residue: 0.2933 time to fit residues: 99.2568 Evaluate side-chains 212 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 633 ASP Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1286 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 418 HIS ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.175378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.164211 restraints weight = 103521.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.166298 restraints weight = 106380.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.166422 restraints weight = 60307.418| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4122 r_free = 0.4122 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.4120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17873 Z= 0.266 Angle : 0.625 10.098 24284 Z= 0.318 Chirality : 0.045 0.382 2735 Planarity : 0.005 0.061 3165 Dihedral : 4.595 22.350 2419 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.54 % Allowed : 15.36 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.66 (0.18), residues: 2221 helix: 1.41 (0.16), residues: 1028 sheet: -0.72 (0.32), residues: 268 loop : -0.19 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 376 HIS 0.007 0.001 HIS B 131 PHE 0.040 0.002 PHE B 375 TYR 0.019 0.002 TYR 11391 ARG 0.015 0.001 ARG C 654 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3560.98 seconds wall clock time: 66 minutes 28.36 seconds (3988.36 seconds total)