Starting phenix.real_space_refine on Sat Jun 14 09:51:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vmi_43357/06_2025/8vmi_43357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vmi_43357/06_2025/8vmi_43357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vmi_43357/06_2025/8vmi_43357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vmi_43357/06_2025/8vmi_43357.map" model { file = "/net/cci-nas-00/data/ceres_data/8vmi_43357/06_2025/8vmi_43357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vmi_43357/06_2025/8vmi_43357.cif" } resolution = 3.1 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= 0.002 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1328 atoms to isotropic. 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 Zn 7 6.06 5 S 96 5.16 5 C 9473 2.51 5 N 2680 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14940 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2924 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 51 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "T" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2340 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 16, 'TRANS': 295} Chain breaks: 6 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 8, 'ASN:plan1': 8, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 153 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4280 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 33, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 202 Chain: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 196 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 25} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 929 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 118} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 139 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11959 SG CYS C 523 118.142 73.682 28.257 1.00 81.35 S ATOM 12004 SG CYS C 530 118.223 75.730 24.531 1.00 97.05 S ATOM 12025 SG CYS C 534 119.033 73.920 25.036 1.00 88.26 S ATOM 12038 SG CYS C 536 115.210 72.206 28.197 1.00 79.31 S ATOM 12090 SG CYS C 543 115.351 76.235 27.794 1.00 67.62 S ATOM 12121 SG CYS C 547 115.682 75.180 30.228 1.00 69.75 S ATOM 12090 SG CYS C 543 115.351 76.235 27.794 1.00 67.62 S ATOM 12136 SG CYS C 549 119.005 79.273 26.528 1.00 80.12 S ATOM 12159 SG CYS C 553 117.166 80.149 25.900 1.00 74.33 S ATOM 12205 SG CYS C 560 99.647 85.526 31.538 1.00 64.89 S ATOM 12222 SG CYS C 562 96.707 87.894 30.522 1.00 65.75 S ATOM 12251 SG CYS C 566 95.968 83.971 30.945 1.00 51.07 S ATOM 12290 SG CYS C 571 97.556 85.338 28.461 1.00 55.82 S ATOM 12205 SG CYS C 560 99.647 85.526 31.538 1.00 64.89 S ATOM 12251 SG CYS C 566 95.968 83.971 30.945 1.00 51.07 S ATOM 12361 SG CYS C 580 98.501 82.791 32.998 1.00 55.94 S ATOM 12419 SG CYS C 588 97.951 86.161 35.106 1.00 62.56 S ATOM 12512 SG CYS C 601 96.499 84.859 35.307 1.00 58.49 S ATOM 12205 SG CYS C 560 99.647 85.526 31.538 1.00 64.89 S ATOM 12303 SG CYS C 573 101.214 83.309 29.715 1.00 56.74 S ATOM 12361 SG CYS C 580 98.501 82.791 32.998 1.00 55.94 S ATOM 12398 SG CYS C 585 102.365 84.146 33.040 1.00 58.84 S ATOM 10970 SG CYS C 286 112.676 70.350 44.565 1.00 66.15 S ATOM 11044 SG CYS C 294 111.580 68.377 44.003 1.00 65.97 S Time building chain proxies: 9.16, per 1000 atoms: 0.61 Number of scatterers: 14940 At special positions: 0 Unit cell: (159.6, 111.3, 103.95, 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) Zn 7 29.99 S 96 16.00 O 2684 8.00 N 2680 7.00 C 9473 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: 3.43 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 534 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 523 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 530 " pdb=" ZN C 802 " pdb="ZN ZN C 802 " - pdb=" SG CYS C 536 " pdb="ZN ZN C 802 " - pdb=" SG CYS C 543 " pdb="ZN ZN C 802 " - pdb=" SG CYS C 547 " pdb=" ZN C 803 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 549 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 553 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 543 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 571 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 566 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 560 " pdb=" ZN C 806 " pdb="ZN ZN C 806 " - pdb=" SG CYS C 560 " pdb="ZN ZN C 806 " - pdb=" SG CYS C 585 " pdb="ZN ZN C 806 " - pdb=" SG CYS C 573 " pdb="ZN ZN C 806 " - pdb=" SG CYS C 580 " pdb=" ZN C 807 " pdb="ZN ZN C 807 " - pdb=" SG CYS C 286 " pdb="ZN ZN C 807 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C 807 " - pdb=" SG CYS C 294 " Number of angles added : 12 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 25.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'L' and resid 575 through 580 removed outlier: 3.726A pdb=" N MET L 579 " --> pdb=" O ARG L 575 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU L 580 " --> pdb=" O PRO L 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 575 through 580' Processing helix chain 'L' and resid 589 through 602 Processing helix chain 'L' and resid 607 through 625 Processing helix chain 'L' and resid 632 through 651 removed outlier: 5.356A pdb=" N GLN L 645 " --> pdb=" O GLU L 641 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS L 646 " --> pdb=" O ASN L 642 " (cutoff:3.500A) Processing helix chain 'L' and resid 652 through 661 removed outlier: 3.856A pdb=" N PHE L 656 " --> pdb=" O LEU L 652 " (cutoff:3.500A) Processing helix chain 'L' and resid 670 through 682 removed outlier: 3.587A pdb=" N ARG L 682 " --> pdb=" O VAL L 678 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 107 Proline residue: T 93 - end of helix removed outlier: 3.914A pdb=" N ILE T 96 " --> pdb=" O LYS T 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR T 102 " --> pdb=" O ARG T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 119 removed outlier: 6.046A pdb=" N THR T 116 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR T 117 " --> pdb=" O THR T 114 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER T 119 " --> pdb=" O THR T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 147 Processing helix chain 'T' and resid 238 through 244 removed outlier: 3.674A pdb=" N MET T 244 " --> pdb=" O SER T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 471 Processing helix chain 'T' and resid 502 through 508 removed outlier: 3.502A pdb=" N ILE T 506 " --> pdb=" O PRO T 503 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG T 508 " --> pdb=" O ASP T 505 " (cutoff:3.500A) Processing helix chain 'T' and resid 539 through 543 removed outlier: 3.536A pdb=" N GLU T 542 " --> pdb=" O SER T 539 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE T 543 " --> pdb=" O MET T 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 539 through 543' Processing helix chain 'N' and resid 5 through 27 Processing helix chain 'N' and resid 28 through 30 No H-bonds generated for 'chain 'N' and resid 28 through 30' Processing helix chain 'N' and resid 155 through 157 No H-bonds generated for 'chain 'N' and resid 155 through 157' Processing helix chain 'N' and resid 304 through 306 No H-bonds generated for 'chain 'N' and resid 304 through 306' Processing helix chain 'N' and resid 348 through 350 No H-bonds generated for 'chain 'N' and resid 348 through 350' Processing helix chain 'N' and resid 355 through 362 removed outlier: 3.646A pdb=" N ASP N 361 " --> pdb=" O GLU N 357 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY N 362 " --> pdb=" O ASP N 358 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 409 Processing helix chain 'C' and resid 15 through 61 Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.603A pdb=" N PHE C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE C 231 " --> pdb=" O ILE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 246 Processing helix chain 'C' and resid 273 through 285 removed outlier: 5.145A pdb=" N SER C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 339 Processing helix chain 'C' and resid 433 through 448 removed outlier: 3.525A pdb=" N THR C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.893A pdb=" N ILE C 454 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 477 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 571 through 576 removed outlier: 4.131A pdb=" N ALA C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 removed outlier: 3.508A pdb=" N ARG C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 661 removed outlier: 3.934A pdb=" N VAL C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 687 Processing helix chain 'C' and resid 729 through 738 Processing helix chain 'F' and resid 144 through 151 Processing helix chain 'F' and resid 157 through 162 Processing helix chain 'P' and resid 191 through 210 Processing helix chain 'P' and resid 245 through 249 removed outlier: 3.916A pdb=" N ILE P 248 " --> pdb=" O PRO P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 259 No H-bonds generated for 'chain 'P' and resid 257 through 259' Processing helix chain 'P' and resid 276 through 281 removed outlier: 3.771A pdb=" N ASP P 281 " --> pdb=" O LEU P 278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 101 removed outlier: 3.566A pdb=" N GLY A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 111 " --> pdb=" O CYS A 126 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU A 125 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 134 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N ARG A 133 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU A 135 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LYS C 99 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A 137 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG C 81 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N CYS A 84 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP A 438 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN A 86 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 424 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE A 418 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 426 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR A 416 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 428 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 154 removed outlier: 3.582A pdb=" N ALA A 166 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 172 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS A 185 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 174 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 181 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 199 removed outlier: 4.014A pdb=" N GLU A 195 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU A 205 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN A 219 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU A 225 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 226 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 294 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 228 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 244 removed outlier: 3.613A pdb=" N PHE A 299 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 315 removed outlier: 3.585A pdb=" N CYS A 311 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A 323 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS A 332 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE A 352 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 370 removed outlier: 3.677A pdb=" N ALA A 378 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 559 through 560 removed outlier: 6.576A pdb=" N THR T 526 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA N 39 " --> pdb=" O THR T 526 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE T 528 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR N 37 " --> pdb=" O ILE T 528 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL T 530 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 34 " --> pdb=" O GLN N 403 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP N 379 " --> pdb=" O VAL N 393 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 203 through 207 removed outlier: 3.504A pdb=" N LEU T 188 " --> pdb=" O VAL T 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 203 through 207 removed outlier: 3.504A pdb=" N LEU T 188 " --> pdb=" O VAL T 206 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL T 191 " --> pdb=" O SER T 247 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER T 247 " --> pdb=" O VAL T 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 354 through 359 removed outlier: 6.891A pdb=" N ILE P 227 " --> pdb=" O ALA T 318 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL P 226 " --> pdb=" O HIS P 242 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS P 242 " --> pdb=" O VAL P 226 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA P 228 " --> pdb=" O LEU P 240 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL P 252 " --> pdb=" O LEU P 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 354 through 359 removed outlier: 6.891A pdb=" N ILE P 227 " --> pdb=" O ALA T 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 474 through 475 removed outlier: 3.994A pdb=" N HIS T 481 " --> pdb=" O GLY T 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 474 through 475 removed outlier: 3.552A pdb=" N ALA T 485 " --> pdb=" O ARG T 427 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE T 491 " --> pdb=" O LEU T 433 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE T 428 " --> pdb=" O ALA T 444 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA T 444 " --> pdb=" O ILE T 428 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA F 141 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU T 443 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AB6, first strand: chain 'N' and resid 77 through 78 removed outlier: 4.660A pdb=" N ASN N 77 " --> pdb=" O HIS N 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 130 through 133 removed outlier: 5.956A pdb=" N ILE N 139 " --> pdb=" O MET N 133 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU N 171 " --> pdb=" O VAL N 151 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG N 172 " --> pdb=" O VAL N 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 180 through 185 removed outlier: 3.501A pdb=" N TRP N 205 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 195 " --> pdb=" O CYS N 203 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR N 221 " --> pdb=" O LEU N 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'N' and resid 280 through 281 removed outlier: 3.617A pdb=" N LEU N 289 " --> pdb=" O TRP N 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 320 through 325 removed outlier: 3.674A pdb=" N PHE N 368 " --> pdb=" O VAL N 344 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 115 removed outlier: 5.538A pdb=" N SER C 114 " --> pdb=" O GLY C 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 614 through 618 Processing sheet with id=AC5, first strand: chain 'C' and resid 637 through 638 removed outlier: 3.545A pdb=" N ILE C 710 " --> pdb=" O ILE C 638 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 644 through 647 529 hydrogen bonds defined for protein. 1464 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: 5.67 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4935 1.34 - 1.46: 3566 1.46 - 1.58: 6662 1.58 - 1.70: 2 1.70 - 1.82: 132 Bond restraints: 15297 Sorted by residual: bond pdb=" CB PRO P 282 " pdb=" CG PRO P 282 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.84e+00 bond pdb=" CB PRO A 110 " pdb=" CG PRO A 110 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.70e+00 bond pdb=" CB PRO C 529 " pdb=" CG PRO C 529 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.00e+00 bond pdb=" CB CYS C 573 " pdb=" SG CYS C 573 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB CYS C 560 " pdb=" SG CYS C 560 " ideal model delta sigma weight residual 1.808 1.770 0.038 3.30e-02 9.18e+02 1.31e+00 ... (remaining 15292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 20535 2.52 - 5.04: 199 5.04 - 7.56: 23 7.56 - 10.09: 7 10.09 - 12.61: 2 Bond angle restraints: 20766 Sorted by residual: angle pdb=" CA PRO P 282 " pdb=" N PRO P 282 " pdb=" CD PRO P 282 " ideal model delta sigma weight residual 112.00 103.68 8.32 1.40e+00 5.10e-01 3.53e+01 angle pdb=" CB MET T 319 " pdb=" CG MET T 319 " pdb=" SD MET T 319 " ideal model delta sigma weight residual 112.70 125.31 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C GLU N 118 " pdb=" N ILE N 119 " pdb=" CA ILE N 119 " ideal model delta sigma weight residual 121.97 128.45 -6.48 1.80e+00 3.09e-01 1.30e+01 angle pdb=" N PHE L 656 " pdb=" CA PHE L 656 " pdb=" C PHE L 656 " ideal model delta sigma weight residual 112.04 106.94 5.10 1.44e+00 4.82e-01 1.25e+01 angle pdb=" CA PRO A 110 " pdb=" N PRO A 110 " pdb=" CD PRO A 110 " ideal model delta sigma weight residual 112.00 107.52 4.48 1.40e+00 5.10e-01 1.02e+01 ... (remaining 20761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 8075 17.58 - 35.16: 833 35.16 - 52.75: 205 52.75 - 70.33: 39 70.33 - 87.91: 8 Dihedral angle restraints: 9160 sinusoidal: 3463 harmonic: 5697 Sorted by residual: dihedral pdb=" CA ALA C 576 " pdb=" C ALA C 576 " pdb=" N VAL C 577 " pdb=" CA VAL C 577 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU N 118 " pdb=" C GLU N 118 " pdb=" N ILE N 119 " pdb=" CA ILE N 119 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA TYR C 574 " pdb=" C TYR C 574 " pdb=" N LEU C 575 " pdb=" CA LEU C 575 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1619 0.041 - 0.083: 484 0.083 - 0.124: 170 0.124 - 0.166: 22 0.166 - 0.207: 1 Chirality restraints: 2296 Sorted by residual: chirality pdb=" CB VAL C 107 " pdb=" CA VAL C 107 " pdb=" CG1 VAL C 107 " pdb=" CG2 VAL C 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE N 119 " pdb=" N ILE N 119 " pdb=" C ILE N 119 " pdb=" CB ILE N 119 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA ILE N 369 " pdb=" N ILE N 369 " pdb=" C ILE N 369 " pdb=" CB ILE N 369 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2293 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 655 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ASN L 655 " -0.074 2.00e-02 2.50e+03 pdb=" O ASN L 655 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE L 656 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP P 281 " -0.063 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO P 282 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO P 282 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO P 282 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 109 " 0.051 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO A 110 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.041 5.00e-02 4.00e+02 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 140 2.55 - 3.14: 11516 3.14 - 3.72: 24000 3.72 - 4.31: 33004 4.31 - 4.90: 55847 Nonbonded interactions: 124507 Sorted by model distance: nonbonded pdb=" SG CYS C 588 " pdb=" SG CYS C 601 " model vdw 1.961 3.760 nonbonded pdb=" OG SER A 210 " pdb=" OD1 ASP A 212 " model vdw 2.107 3.040 nonbonded pdb=" NH1 ARG T 103 " pdb=" OE2 GLU N 13 " model vdw 2.117 3.120 nonbonded pdb=" OE2 GLU A 90 " pdb=" OH TYR A 124 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR T 117 " pdb=" OD1 ASN N 27 " model vdw 2.173 3.040 ... (remaining 124502 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.960 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.005 0.474 15317 Z= 0.194 Angle : 0.718 24.124 20778 Z= 0.321 Chirality : 0.044 0.207 2296 Planarity : 0.005 0.091 2679 Dihedral : 15.497 87.910 5440 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.46 % Allowed : 21.04 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1901 helix: 0.89 (0.26), residues: 409 sheet: -0.51 (0.25), residues: 463 loop : -1.03 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 499 HIS 0.006 0.001 HIS N 71 PHE 0.012 0.001 PHE T 86 TYR 0.020 0.001 TYR T 117 ARG 0.011 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.20411 ( 513) hydrogen bonds : angle 8.09634 ( 1464) metal coordination : bond 0.10718 ( 20) metal coordination : angle 14.68125 ( 12) covalent geometry : bond 0.00365 (15297) covalent geometry : angle 0.62587 (20766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 234 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: T 204 ARG cc_start: 0.7353 (ptm-80) cc_final: 0.7071 (ptm-80) REVERT: C 31 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7637 (ptp90) REVERT: C 502 HIS cc_start: 0.7322 (t70) cc_final: 0.7064 (t-170) REVERT: C 561 ARG cc_start: 0.5656 (ppt170) cc_final: 0.5107 (ppt170) REVERT: P 201 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6939 (mtm110) outliers start: 7 outliers final: 4 residues processed: 236 average time/residue: 0.3274 time to fit residues: 108.2273 Evaluate side-chains 222 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 217 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 655 ASN Chi-restraints excluded: chain L residue 656 PHE Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain C residue 31 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 172 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN C 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135285 restraints weight = 19356.346| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.55 r_work: 0.3437 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15317 Z= 0.174 Angle : 0.668 19.997 20778 Z= 0.326 Chirality : 0.045 0.171 2296 Planarity : 0.004 0.058 2679 Dihedral : 5.523 59.072 2093 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.01 % Allowed : 19.07 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1901 helix: 1.03 (0.26), residues: 411 sheet: -0.58 (0.24), residues: 455 loop : -1.09 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 218 HIS 0.006 0.001 HIS N 71 PHE 0.014 0.002 PHE T 357 TYR 0.018 0.001 TYR A 148 ARG 0.004 0.000 ARG C 685 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 513) hydrogen bonds : angle 5.87432 ( 1464) metal coordination : bond 0.01250 ( 20) metal coordination : angle 9.55676 ( 12) covalent geometry : bond 0.00414 (15297) covalent geometry : angle 0.62798 (20766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 247 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8383 (m-70) REVERT: A 307 ASN cc_start: 0.8592 (t0) cc_final: 0.8375 (t0) REVERT: L 601 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6826 (mm-30) REVERT: L 641 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: T 117 TYR cc_start: 0.8448 (p90) cc_final: 0.7724 (p90) REVERT: T 185 GLU cc_start: 0.8163 (pm20) cc_final: 0.7765 (pm20) REVERT: T 190 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7485 (mtmm) REVERT: T 443 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7851 (tm-30) REVERT: N 27 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8464 (m-40) REVERT: N 320 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (mp) REVERT: N 322 GLN cc_start: 0.7914 (tp40) cc_final: 0.7609 (tp40) REVERT: N 324 GLN cc_start: 0.7959 (mm110) cc_final: 0.7586 (mt0) REVERT: N 357 GLU cc_start: 0.7221 (pm20) cc_final: 0.6886 (pm20) REVERT: C 24 MET cc_start: 0.8660 (mmp) cc_final: 0.8265 (mmp) REVERT: C 121 MET cc_start: 0.8270 (tpt) cc_final: 0.8038 (tpp) REVERT: I 26 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7879 (mtt180) outliers start: 61 outliers final: 33 residues processed: 290 average time/residue: 0.3063 time to fit residues: 126.2201 Evaluate side-chains 264 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain T residue 529 LEU Chi-restraints excluded: chain T residue 531 CYS Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 270 SER Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain I residue 26 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 624 HIS L 655 ASN T 351 GLN N 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135258 restraints weight = 19502.418| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.57 r_work: 0.3436 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15317 Z= 0.178 Angle : 0.658 20.184 20778 Z= 0.322 Chirality : 0.045 0.183 2296 Planarity : 0.004 0.057 2679 Dihedral : 5.279 59.719 2085 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.73 % Allowed : 19.79 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1901 helix: 1.03 (0.26), residues: 409 sheet: -0.75 (0.24), residues: 468 loop : -1.16 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 218 HIS 0.005 0.001 HIS N 71 PHE 0.013 0.002 PHE T 86 TYR 0.017 0.001 TYR A 148 ARG 0.003 0.000 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 513) hydrogen bonds : angle 5.66544 ( 1464) metal coordination : bond 0.01233 ( 20) metal coordination : angle 8.65434 ( 12) covalent geometry : bond 0.00426 (15297) covalent geometry : angle 0.62397 (20766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ASN cc_start: 0.8586 (t0) cc_final: 0.8360 (t0) REVERT: L 601 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6991 (mm-30) REVERT: L 641 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: T 106 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8604 (mp) REVERT: T 117 TYR cc_start: 0.8510 (p90) cc_final: 0.8300 (p90) REVERT: T 166 HIS cc_start: 0.7147 (t-90) cc_final: 0.6937 (t70) REVERT: T 185 GLU cc_start: 0.8155 (pm20) cc_final: 0.7665 (pm20) REVERT: T 190 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7456 (mtmm) REVERT: T 443 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7879 (tm-30) REVERT: T 514 PHE cc_start: 0.8016 (m-10) cc_final: 0.7577 (m-10) REVERT: N 200 HIS cc_start: 0.6890 (m-70) cc_final: 0.6600 (m-70) REVERT: N 223 PHE cc_start: 0.8085 (m-80) cc_final: 0.7820 (m-80) REVERT: N 320 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8432 (mp) REVERT: N 357 GLU cc_start: 0.7290 (pm20) cc_final: 0.6956 (pm20) REVERT: C 24 MET cc_start: 0.8568 (mmp) cc_final: 0.8131 (mmp) REVERT: C 99 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6445 (ptmt) REVERT: C 502 HIS cc_start: 0.7382 (t-170) cc_final: 0.7117 (t-170) outliers start: 72 outliers final: 42 residues processed: 282 average time/residue: 0.3243 time to fit residues: 129.4254 Evaluate side-chains 271 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 201 CYS Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain T residue 531 CYS Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN L 655 ASN T 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136642 restraints weight = 19503.827| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.34 r_work: 0.3410 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15317 Z= 0.181 Angle : 0.660 21.202 20778 Z= 0.322 Chirality : 0.045 0.187 2296 Planarity : 0.004 0.056 2679 Dihedral : 5.302 57.973 2085 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.87 % Allowed : 20.32 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1901 helix: 1.09 (0.26), residues: 410 sheet: -0.78 (0.24), residues: 459 loop : -1.17 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 218 HIS 0.008 0.001 HIS A 160 PHE 0.013 0.002 PHE C 724 TYR 0.018 0.001 TYR A 148 ARG 0.006 0.000 ARG T 508 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 513) hydrogen bonds : angle 5.53031 ( 1464) metal coordination : bond 0.01225 ( 20) metal coordination : angle 8.46109 ( 12) covalent geometry : bond 0.00434 (15297) covalent geometry : angle 0.62784 (20766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 3.131 Fit side-chains REVERT: A 213 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8528 (m-70) REVERT: A 307 ASN cc_start: 0.8619 (t0) cc_final: 0.8372 (t0) REVERT: L 601 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7095 (mm-30) REVERT: T 106 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8685 (mp) REVERT: T 185 GLU cc_start: 0.8173 (pm20) cc_final: 0.7639 (pm20) REVERT: T 190 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7495 (mtmm) REVERT: T 204 ARG cc_start: 0.7718 (ptm-80) cc_final: 0.7374 (ptm-80) REVERT: T 360 ARG cc_start: 0.8045 (tmm-80) cc_final: 0.7680 (ttp80) REVERT: T 443 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7982 (tm-30) REVERT: T 514 PHE cc_start: 0.8013 (m-10) cc_final: 0.7652 (m-10) REVERT: N 200 HIS cc_start: 0.6907 (m-70) cc_final: 0.6614 (m-70) REVERT: N 223 PHE cc_start: 0.8101 (m-80) cc_final: 0.7844 (m-80) REVERT: N 320 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8455 (mp) REVERT: N 357 GLU cc_start: 0.7362 (pm20) cc_final: 0.7060 (pm20) REVERT: C 24 MET cc_start: 0.8660 (mmp) cc_final: 0.8157 (mmp) REVERT: C 39 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8330 (mtpp) REVERT: C 99 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6622 (ptmt) REVERT: C 502 HIS cc_start: 0.7461 (t-170) cc_final: 0.7168 (t-170) REVERT: C 561 ARG cc_start: 0.6394 (ppt170) cc_final: 0.5467 (ptt90) REVERT: P 201 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7358 (mtm110) outliers start: 74 outliers final: 49 residues processed: 283 average time/residue: 0.3724 time to fit residues: 152.7620 Evaluate side-chains 272 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 659 HIS Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain T residue 529 LEU Chi-restraints excluded: chain T residue 531 CYS Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 365 GLU Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 133 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 620 HIS L 655 ASN T 156 HIS T 351 GLN C 607 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133832 restraints weight = 19739.201| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.38 r_work: 0.3371 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15317 Z= 0.241 Angle : 0.719 25.752 20778 Z= 0.349 Chirality : 0.047 0.198 2296 Planarity : 0.005 0.058 2679 Dihedral : 5.385 55.416 2085 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.59 % Allowed : 20.38 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.19), residues: 1901 helix: 0.91 (0.26), residues: 411 sheet: -0.86 (0.24), residues: 451 loop : -1.25 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 388 HIS 0.007 0.001 HIS N 71 PHE 0.016 0.002 PHE C 451 TYR 0.020 0.002 TYR A 148 ARG 0.007 0.000 ARG T 508 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 513) hydrogen bonds : angle 5.59165 ( 1464) metal coordination : bond 0.01486 ( 20) metal coordination : angle 9.75749 ( 12) covalent geometry : bond 0.00578 (15297) covalent geometry : angle 0.67980 (20766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 226 time to evaluate : 1.591 Fit side-chains REVERT: A 213 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8604 (m-70) REVERT: L 641 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: T 106 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8741 (mp) REVERT: T 117 TYR cc_start: 0.8453 (p90) cc_final: 0.8247 (p90) REVERT: T 185 GLU cc_start: 0.8107 (pm20) cc_final: 0.7420 (pm20) REVERT: T 190 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7470 (mtmm) REVERT: T 443 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8007 (tm-30) REVERT: N 200 HIS cc_start: 0.7056 (m-70) cc_final: 0.6693 (m-70) REVERT: N 320 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8474 (mp) REVERT: N 357 GLU cc_start: 0.7420 (pm20) cc_final: 0.7124 (pm20) REVERT: N 367 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7683 (pt) REVERT: C 24 MET cc_start: 0.8583 (mmp) cc_final: 0.8083 (mmp) REVERT: C 39 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8355 (mtpp) REVERT: C 76 SER cc_start: 0.7493 (OUTLIER) cc_final: 0.7245 (t) REVERT: C 99 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6668 (ptmt) REVERT: C 230 MET cc_start: 0.5454 (mtt) cc_final: 0.4917 (mpp) REVERT: C 499 TRP cc_start: 0.7998 (t60) cc_final: 0.7779 (t60) REVERT: C 561 ARG cc_start: 0.6483 (ppt170) cc_final: 0.5592 (ptt90) REVERT: C 735 LYS cc_start: 0.8910 (tttt) cc_final: 0.8653 (tttt) REVERT: P 201 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7493 (mtm-85) outliers start: 85 outliers final: 53 residues processed: 290 average time/residue: 0.2894 time to fit residues: 120.3355 Evaluate side-chains 279 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 659 HIS Chi-restraints excluded: chain L residue 673 SER Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 191 VAL Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain T residue 531 CYS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 365 GLU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 163 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN A 374 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 655 ASN ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 GLN ** N 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.175035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134199 restraints weight = 19625.619| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.57 r_work: 0.3399 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15317 Z= 0.168 Angle : 0.673 23.756 20778 Z= 0.326 Chirality : 0.045 0.186 2296 Planarity : 0.004 0.057 2679 Dihedral : 5.147 58.182 2082 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.40 % Allowed : 22.55 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.94 (0.19), residues: 1901 helix: 1.02 (0.26), residues: 413 sheet: -0.80 (0.25), residues: 444 loop : -1.22 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 218 HIS 0.012 0.001 HIS N 226 PHE 0.018 0.002 PHE C 32 TYR 0.017 0.001 TYR T 117 ARG 0.006 0.000 ARG T 508 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 513) hydrogen bonds : angle 5.45401 ( 1464) metal coordination : bond 0.01161 ( 20) metal coordination : angle 8.98439 ( 12) covalent geometry : bond 0.00402 (15297) covalent geometry : angle 0.63752 (20766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 1.843 Fit side-chains revert: symmetry clash REVERT: A 213 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8540 (m-70) REVERT: A 355 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7555 (ptp-110) REVERT: A 374 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: L 641 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: T 106 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8753 (mp) REVERT: T 185 GLU cc_start: 0.8127 (pm20) cc_final: 0.7385 (pm20) REVERT: T 190 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7429 (mtmm) REVERT: T 360 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7330 (ttp80) REVERT: T 443 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7983 (tm-30) REVERT: T 514 PHE cc_start: 0.8060 (m-80) cc_final: 0.7697 (m-10) REVERT: N 200 HIS cc_start: 0.6866 (m-70) cc_final: 0.6530 (m-70) REVERT: N 320 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8473 (mp) REVERT: N 367 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7657 (pt) REVERT: C 24 MET cc_start: 0.8738 (mmp) cc_final: 0.8311 (mmp) REVERT: C 39 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8341 (mtpp) REVERT: C 99 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6585 (ptmt) REVERT: C 230 MET cc_start: 0.5546 (mtt) cc_final: 0.5039 (mpp) REVERT: C 735 LYS cc_start: 0.8890 (tttt) cc_final: 0.8620 (tttt) outliers start: 67 outliers final: 49 residues processed: 270 average time/residue: 0.3026 time to fit residues: 116.3423 Evaluate side-chains 270 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 659 HIS Chi-restraints excluded: chain L residue 673 SER Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 191 VAL Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 295 PHE Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 365 GLU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 153 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 655 ASN ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.175008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135559 restraints weight = 19643.294| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.64 r_work: 0.3407 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15317 Z= 0.174 Angle : 0.676 23.122 20778 Z= 0.327 Chirality : 0.045 0.186 2296 Planarity : 0.004 0.061 2679 Dihedral : 5.125 59.622 2082 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.52 % Allowed : 22.02 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1901 helix: 1.00 (0.26), residues: 413 sheet: -0.87 (0.24), residues: 468 loop : -1.23 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 499 HIS 0.010 0.001 HIS N 226 PHE 0.015 0.002 PHE C 32 TYR 0.017 0.001 TYR A 148 ARG 0.009 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 513) hydrogen bonds : angle 5.41565 ( 1464) metal coordination : bond 0.01144 ( 20) metal coordination : angle 8.75998 ( 12) covalent geometry : bond 0.00419 (15297) covalent geometry : angle 0.64245 (20766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 213 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8533 (m-70) REVERT: L 601 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7040 (mm-30) REVERT: L 641 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: L 650 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7012 (mppt) REVERT: T 106 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8732 (mp) REVERT: T 185 GLU cc_start: 0.8161 (pm20) cc_final: 0.7308 (pm20) REVERT: T 190 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7401 (mtmm) REVERT: T 360 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7342 (ttp80) REVERT: T 431 GLN cc_start: 0.8243 (mt0) cc_final: 0.7972 (mm110) REVERT: T 443 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7891 (tm-30) REVERT: T 514 PHE cc_start: 0.8068 (m-80) cc_final: 0.7776 (m-10) REVERT: N 66 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8023 (mm) REVERT: N 200 HIS cc_start: 0.6856 (m-70) cc_final: 0.6538 (m-70) REVERT: N 320 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8451 (mp) REVERT: N 367 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7671 (pt) REVERT: C 24 MET cc_start: 0.8753 (mmp) cc_final: 0.8318 (mmp) REVERT: C 39 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8356 (mtpp) REVERT: C 99 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6653 (ptmt) REVERT: C 230 MET cc_start: 0.5594 (mtt) cc_final: 0.5150 (mpp) REVERT: C 502 HIS cc_start: 0.7507 (t70) cc_final: 0.7181 (t-170) REVERT: C 735 LYS cc_start: 0.8867 (tttt) cc_final: 0.8591 (tttt) outliers start: 84 outliers final: 64 residues processed: 282 average time/residue: 0.3613 time to fit residues: 145.8828 Evaluate side-chains 285 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 213 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 637 MET Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain L residue 650 LYS Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 659 HIS Chi-restraints excluded: chain L residue 673 SER Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 189 VAL Chi-restraints excluded: chain T residue 191 VAL Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 365 GLU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Chi-restraints excluded: chain I residue 26 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 21 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN L 655 ASN ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 GLN ** P 283 ASN ** 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 = 0.4115 r_free = 0.4115 target = 0.175124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135887 restraints weight = 19558.586| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.79 r_work: 0.3400 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15317 Z= 0.164 Angle : 0.674 22.686 20778 Z= 0.326 Chirality : 0.045 0.191 2296 Planarity : 0.004 0.056 2679 Dihedral : 5.074 58.207 2082 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.52 % Allowed : 22.16 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1901 helix: 1.07 (0.26), residues: 413 sheet: -0.97 (0.24), residues: 477 loop : -1.16 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 499 HIS 0.008 0.001 HIS N 226 PHE 0.014 0.002 PHE C 32 TYR 0.017 0.001 TYR A 148 ARG 0.007 0.000 ARG T 508 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 513) hydrogen bonds : angle 5.33970 ( 1464) metal coordination : bond 0.01092 ( 20) metal coordination : angle 8.64202 ( 12) covalent geometry : bond 0.00393 (15297) covalent geometry : angle 0.64093 (20766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 221 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: A 213 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8452 (m-70) REVERT: A 307 ASN cc_start: 0.8557 (t0) cc_final: 0.8303 (t0) REVERT: L 641 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: L 650 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7068 (mppt) REVERT: T 106 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8655 (mp) REVERT: T 185 GLU cc_start: 0.8202 (pm20) cc_final: 0.7368 (pm20) REVERT: T 190 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7343 (mtmm) REVERT: T 431 GLN cc_start: 0.8139 (mt0) cc_final: 0.7867 (mm110) REVERT: T 443 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7787 (tm-30) REVERT: T 514 PHE cc_start: 0.8021 (m-80) cc_final: 0.7730 (m-10) REVERT: N 66 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7839 (mm) REVERT: N 223 PHE cc_start: 0.8107 (m-80) cc_final: 0.7902 (m-80) REVERT: N 320 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8335 (mp) REVERT: N 367 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7541 (pt) REVERT: C 24 MET cc_start: 0.8731 (mmp) cc_final: 0.8318 (mmp) REVERT: C 39 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8202 (mtpp) REVERT: C 99 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6554 (ptmt) REVERT: C 116 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7654 (tp) REVERT: C 230 MET cc_start: 0.5396 (mtt) cc_final: 0.5094 (mpp) REVERT: C 502 HIS cc_start: 0.7152 (t70) cc_final: 0.6912 (t-170) REVERT: C 735 LYS cc_start: 0.8829 (tttt) cc_final: 0.8592 (tttt) outliers start: 84 outliers final: 66 residues processed: 282 average time/residue: 0.3367 time to fit residues: 135.8081 Evaluate side-chains 291 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 637 MET Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain L residue 650 LYS Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 659 HIS Chi-restraints excluded: chain L residue 673 SER Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 189 VAL Chi-restraints excluded: chain T residue 191 VAL Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain T residue 531 CYS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 328 HIS Chi-restraints excluded: chain N residue 365 GLU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Chi-restraints excluded: chain I residue 26 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 655 ASN ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 GLN ** P 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.174837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135566 restraints weight = 19535.210| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.64 r_work: 0.3405 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 15317 Z= 0.185 Angle : 0.697 23.079 20778 Z= 0.336 Chirality : 0.046 0.187 2296 Planarity : 0.004 0.056 2679 Dihedral : 5.143 59.081 2082 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.59 % Allowed : 22.62 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1901 helix: 1.04 (0.26), residues: 413 sheet: -1.01 (0.23), residues: 487 loop : -1.17 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 499 HIS 0.008 0.001 HIS N 226 PHE 0.020 0.002 PHE C 469 TYR 0.018 0.002 TYR A 148 ARG 0.008 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 513) hydrogen bonds : angle 5.34511 ( 1464) metal coordination : bond 0.01161 ( 20) metal coordination : angle 8.86925 ( 12) covalent geometry : bond 0.00448 (15297) covalent geometry : angle 0.66342 (20766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 222 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.7839 (pt0) cc_final: 0.7564 (pt0) REVERT: A 213 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8536 (m-70) REVERT: A 307 ASN cc_start: 0.8611 (t0) cc_final: 0.8333 (t0) REVERT: A 355 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7543 (ptp-110) REVERT: L 641 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: T 106 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8674 (mp) REVERT: T 190 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7437 (mtmm) REVERT: T 431 GLN cc_start: 0.8269 (mt0) cc_final: 0.8026 (mm110) REVERT: T 443 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7905 (tm-30) REVERT: T 514 PHE cc_start: 0.8054 (m-80) cc_final: 0.7767 (m-10) REVERT: N 66 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8041 (mm) REVERT: N 200 HIS cc_start: 0.6883 (m-70) cc_final: 0.6570 (m-70) REVERT: N 223 PHE cc_start: 0.8128 (m-80) cc_final: 0.7915 (m-80) REVERT: N 320 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8450 (mp) REVERT: N 367 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7667 (pt) REVERT: C 24 MET cc_start: 0.8704 (mmp) cc_final: 0.8323 (mmp) REVERT: C 39 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8370 (mtpp) REVERT: C 76 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.7243 (t) REVERT: C 99 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6696 (ptmt) REVERT: C 116 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7763 (tp) REVERT: C 230 MET cc_start: 0.5481 (mtt) cc_final: 0.5215 (mpp) REVERT: C 502 HIS cc_start: 0.7360 (t70) cc_final: 0.7054 (t-170) REVERT: P 288 MET cc_start: 0.7328 (mmm) cc_final: 0.7084 (mmm) outliers start: 85 outliers final: 69 residues processed: 285 average time/residue: 0.3183 time to fit residues: 129.0292 Evaluate side-chains 296 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 217 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 637 MET Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 659 HIS Chi-restraints excluded: chain L residue 673 SER Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 189 VAL Chi-restraints excluded: chain T residue 191 VAL Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain T residue 531 CYS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 365 GLU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Chi-restraints excluded: chain I residue 26 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 189 optimal weight: 0.0020 chunk 121 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 655 ASN ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135659 restraints weight = 19693.294| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.59 r_work: 0.3397 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15317 Z= 0.181 Angle : 0.702 23.073 20778 Z= 0.338 Chirality : 0.046 0.186 2296 Planarity : 0.004 0.056 2679 Dihedral : 5.146 59.882 2082 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.39 % Allowed : 22.55 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1901 helix: 1.06 (0.26), residues: 413 sheet: -0.87 (0.24), residues: 458 loop : -1.21 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 499 HIS 0.008 0.001 HIS N 226 PHE 0.021 0.002 PHE C 469 TYR 0.017 0.002 TYR A 148 ARG 0.011 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 513) hydrogen bonds : angle 5.32380 ( 1464) metal coordination : bond 0.01129 ( 20) metal coordination : angle 8.88373 ( 12) covalent geometry : bond 0.00437 (15297) covalent geometry : angle 0.66870 (20766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3802 Ramachandran restraints generated. 1901 Oldfield, 0 Emsley, 1901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 221 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.7856 (pt0) cc_final: 0.7583 (pt0) REVERT: A 213 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8547 (m-70) REVERT: A 307 ASN cc_start: 0.8594 (t0) cc_final: 0.8319 (t0) REVERT: A 355 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7569 (ptp-110) REVERT: L 601 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7229 (mm-30) REVERT: L 641 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: T 106 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8637 (mp) REVERT: T 185 GLU cc_start: 0.8068 (pm20) cc_final: 0.7788 (pm20) REVERT: T 190 LYS cc_start: 0.7716 (mtmt) cc_final: 0.7401 (mtmm) REVERT: T 431 GLN cc_start: 0.8271 (mt0) cc_final: 0.8032 (mm110) REVERT: T 443 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7919 (tm-30) REVERT: T 514 PHE cc_start: 0.8060 (m-80) cc_final: 0.7782 (m-10) REVERT: N 66 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8103 (mm) REVERT: N 76 GLN cc_start: 0.7730 (tp40) cc_final: 0.7421 (tp40) REVERT: N 223 PHE cc_start: 0.8133 (m-80) cc_final: 0.7880 (m-80) REVERT: N 255 TRP cc_start: 0.8899 (m100) cc_final: 0.7796 (m100) REVERT: N 320 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8453 (mp) REVERT: N 367 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7670 (pt) REVERT: C 24 MET cc_start: 0.8830 (mmp) cc_final: 0.8411 (mmp) REVERT: C 39 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8363 (mtpp) REVERT: C 76 SER cc_start: 0.7459 (OUTLIER) cc_final: 0.7238 (t) REVERT: C 99 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6722 (ptmt) REVERT: C 116 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7769 (tp) REVERT: C 230 MET cc_start: 0.6032 (mtt) cc_final: 0.5716 (mpp) REVERT: C 502 HIS cc_start: 0.7450 (t70) cc_final: 0.7116 (t-170) REVERT: P 288 MET cc_start: 0.7203 (mmm) cc_final: 0.6863 (mmm) outliers start: 82 outliers final: 70 residues processed: 281 average time/residue: 0.3542 time to fit residues: 143.4386 Evaluate side-chains 299 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 219 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain L residue 596 THR Chi-restraints excluded: chain L residue 637 MET Chi-restraints excluded: chain L residue 641 GLU Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 659 HIS Chi-restraints excluded: chain L residue 673 SER Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 189 VAL Chi-restraints excluded: chain T residue 191 VAL Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 300 THR Chi-restraints excluded: chain T residue 438 THR Chi-restraints excluded: chain T residue 531 CYS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 239 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 365 GLU Chi-restraints excluded: chain N residue 367 LEU Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 400 GLN Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 620 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain P residue 206 ASN Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 270 SER Chi-restraints excluded: chain I residue 26 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 146 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 118 optimal weight: 50.0000 chunk 180 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 1 optimal weight: 0.0170 chunk 11 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 655 ASN ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 GLN ** N 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136664 restraints weight = 19551.766| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.74 r_work: 0.3422 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 15317 Z= 0.160 Angle : 0.686 22.333 20778 Z= 0.330 Chirality : 0.045 0.183 2296 Planarity : 0.004 0.056 2679 Dihedral : 5.046 59.564 2082 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.39 % Allowed : 22.88 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1901 helix: 1.13 (0.26), residues: 412 sheet: -0.78 (0.24), residues: 452 loop : -1.18 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 499 HIS 0.011 0.001 HIS N 176 PHE 0.021 0.002 PHE C 469 TYR 0.018 0.001 TYR A 148 ARG 0.011 0.000 ARG C 31 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 513) hydrogen bonds : angle 5.27267 ( 1464) metal coordination : bond 0.01030 ( 20) metal coordination : angle 8.52896 ( 12) covalent geometry : bond 0.00386 (15297) covalent geometry : angle 0.65460 (20766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10288.86 seconds wall clock time: 184 minutes 41.60 seconds (11081.60 seconds total)