Starting phenix.real_space_refine on Sat Aug 8 14:05:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.cif" model { file = "/net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rec_19082/08_2026/8rec_19082.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 104 5.49 5 Mg 1 5.21 5 S 101 5.16 5 C 17842 2.51 5 N 5131 2.21 5 O 5784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28965 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 934 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "R" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 151 Classifications: {'RNAv2': 7} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna3p': 6} Chain: "T" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1053 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 22, 'ARG:plan': 18, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 15, 'PHE:plan': 5, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9654 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 721 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'ASN:plan1': 6, 'TYR:plan': 4, 'ARG:plan': 19, 'PHE:plan': 10, 'ASP:plan': 18, 'GLU:plan': 31, 'HIS:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 462 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2444 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'GLN:plan1': 4, 'GLU:plan': 12, 'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 170 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16813 SG CYS D 70 103.988 112.897 92.800 1.00 53.34 S ATOM 16942 SG CYS D 88 102.502 113.956 95.648 1.00 55.08 S ATOM 23055 SG CYS D 898 95.785 46.619 85.899 1.00 31.02 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.66 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.66 Time building chain proxies: 5.13, per 1000 atoms: 0.18 Number of scatterers: 28965 At special positions: 0 Unit cell: (142.04, 170.66, 164.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 101 16.00 P 104 15.00 Mg 1 11.99 O 5784 8.00 N 5131 7.00 C 17842 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6742 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 43 sheets defined 39.7% alpha, 13.9% beta 39 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.911A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.713A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.191A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.747A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.560A pdb=" N LEU A 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.501A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.652A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.757A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.360A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.565A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.784A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.650A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.678A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.942A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.903A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.270A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.689A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.748A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.724A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.979A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.584A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.509A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.827A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.098A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.042A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.610A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 4.068A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.632A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.987A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.755A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.534A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.899A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.202A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.797A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 4.065A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.025A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.777A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.604A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.585A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.624A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.619A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.565A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.016A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.726A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.938A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.691A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.912A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.300A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.645A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.692A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.555A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.560A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.685A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.556A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 4.158A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.319A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 232 through 239 removed outlier: 3.760A pdb=" N MET M 236 " --> pdb=" O PHE M 232 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.686A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 265 removed outlier: 3.642A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 351 Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.596A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 384 removed outlier: 3.960A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 464 removed outlier: 4.204A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.575A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 111 removed outlier: 3.626A pdb=" N GLY A 106 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA A 138 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY A 108 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N GLU A 136 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 12.090A pdb=" N VAL A 110 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N THR A 134 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 19 removed outlier: 5.396A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.834A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.556A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.873A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.873A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB2, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB4, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB5, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.072A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.781A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AB9, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.533A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 5.338A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 798 through 804 removed outlier: 8.582A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.487A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 841 Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.782A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.798A pdb=" N GLU C1340 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.693A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 111 removed outlier: 8.377A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.691A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.110A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.840A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 957 through 958 Processing sheet with id=AE3, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE4, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.818A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 4.652A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE7, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.276A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 1128 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 7.82 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.15: 1 1.15 - 1.32: 4871 1.32 - 1.48: 11810 1.48 - 1.65: 12738 1.65 - 1.81: 176 Bond restraints: 29596 Sorted by residual: bond pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 1.492 0.987 0.505 5.00e-02 4.00e+02 1.02e+02 bond pdb=" CG PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 1.503 1.213 0.290 3.40e-02 8.65e+02 7.29e+01 bond pdb=" CG PRO M 211 " pdb=" CD PRO M 211 " ideal model delta sigma weight residual 1.503 1.215 0.288 3.40e-02 8.65e+02 7.15e+01 bond pdb=" N PRO M 211 " pdb=" CD PRO M 211 " ideal model delta sigma weight residual 1.473 1.552 -0.079 1.40e-02 5.10e+03 3.16e+01 bond pdb=" C1' DT N 4 " pdb=" N1 DT N 4 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.55e+01 ... (remaining 29591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 40636 14.77 - 29.53: 2 29.53 - 44.30: 1 44.30 - 59.06: 0 59.06 - 73.83: 1 Bond angle restraints: 40640 Sorted by residual: angle pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO M 258 " pdb=" CD PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 103.20 75.94 27.26 1.50e+00 4.44e-01 3.30e+02 angle pdb=" CA PRO M 258 " pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 104.50 72.68 31.82 1.90e+00 2.77e-01 2.80e+02 angle pdb=" CA PRO M 211 " pdb=" N PRO M 211 " pdb=" CD PRO M 211 " ideal model delta sigma weight residual 112.00 93.76 18.24 1.40e+00 5.10e-01 1.70e+02 angle pdb=" N PRO M 211 " pdb=" CD PRO M 211 " pdb=" CG PRO M 211 " ideal model delta sigma weight residual 103.20 89.59 13.61 1.50e+00 4.44e-01 8.23e+01 ... (remaining 40635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 16868 35.43 - 70.86: 879 70.86 - 106.28: 37 106.28 - 141.71: 0 141.71 - 177.14: 2 Dihedral angle restraints: 17786 sinusoidal: 7336 harmonic: 10450 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 141.98 38.02 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" O5' C R 1 " pdb=" C5' C R 1 " pdb=" C4' C R 1 " pdb=" C3' C R 1 " ideal model delta sinusoidal sigma weight residual 60.00 28.59 31.41 3 6.40e+00 2.44e-02 2.80e+01 dihedral pdb=" C4' DT N 6 " pdb=" C3' DT N 6 " pdb=" O3' DT N 6 " pdb=" P DC N 7 " ideal model delta sinusoidal sigma weight residual 220.00 42.86 177.14 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 17783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4170 0.064 - 0.128: 621 0.128 - 0.191: 21 0.191 - 0.255: 10 0.255 - 0.319: 1 Chirality restraints: 4823 Sorted by residual: chirality pdb=" CA PRO M 211 " pdb=" N PRO M 211 " pdb=" C PRO M 211 " pdb=" CB PRO M 211 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" P G R -1 " pdb=" OP1 G R -1 " pdb=" OP2 G R -1 " pdb=" O5' G R -1 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" P G R 4 " pdb=" OP1 G R 4 " pdb=" OP2 G R 4 " pdb=" O5' G R 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4820 not shown) Planarity restraints: 4964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 210 " 0.094 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO M 211 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO M 211 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO M 211 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 468 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO M 469 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO M 469 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO M 469 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 854 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO C 855 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 855 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 855 " 0.043 5.00e-02 4.00e+02 ... (remaining 4961 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 229 2.59 - 3.17: 24141 3.17 - 3.74: 45740 3.74 - 4.32: 59932 4.32 - 4.90: 99498 Nonbonded interactions: 229540 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.010 2.170 nonbonded pdb=" O3' A R 5 " pdb="MG MG D1501 " model vdw 2.049 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.057 2.170 nonbonded pdb=" O LEU D 71 " pdb="ZN ZN D1502 " model vdw 2.140 2.230 nonbonded pdb=" OG SER C 4 " pdb=" OE1 GLU C 7 " model vdw 2.150 3.040 ... (remaining 229535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 0.505 29599 Z= 0.248 Angle : 0.791 73.826 40640 Z= 0.444 Chirality : 0.044 0.319 4823 Planarity : 0.005 0.125 4964 Dihedral : 19.125 177.140 11044 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 0.37 % Allowed : 28.28 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3609 helix: 1.00 (0.15), residues: 1254 sheet: 0.17 (0.26), residues: 391 loop : -1.47 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1140 TYR 0.017 0.001 TYR A 185 PHE 0.014 0.001 PHE A 231 TRP 0.011 0.001 TRP C 183 HIS 0.012 0.001 HIS M 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.25 (29596) covalent geometry : angle 0.79106 / 0.44 (40640) hydrogen bonds : bond 0.15646 / 16.11 ( 1213) hydrogen bonds : angle 5.78146 / 7.59 ( 3360) metal coordination : bond 0.00070 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 327 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 264 ASP cc_start: 0.6729 (p0) cc_final: 0.6152 (p0) REVERT: M 365 MET cc_start: 0.6177 (tpp) cc_final: 0.5617 (tpp) REVERT: M 376 MET cc_start: -0.1022 (tpt) cc_final: -0.1361 (tpt) outliers start: 10 outliers final: 6 residues processed: 332 average time/residue: 0.1682 time to fit residues: 89.3395 Evaluate side-chains 226 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 391 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 50.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN B 147 GLN C 620 ASN C 658 GLN C1009 ASN D 477 GLN D1227 HIS D1249 ASN D1259 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.089477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.058440 restraints weight = 97504.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060434 restraints weight = 45298.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.061687 restraints weight = 28453.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.062439 restraints weight = 21651.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062844 restraints weight = 18581.232| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29599 Z= 0.149 Angle : 0.614 10.400 40640 Z= 0.322 Chirality : 0.043 0.375 4823 Planarity : 0.005 0.075 4964 Dihedral : 16.397 177.527 5086 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 3.80 % Allowed : 25.75 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3609 helix: 1.11 (0.15), residues: 1290 sheet: 0.13 (0.27), residues: 383 loop : -1.42 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.030 0.001 TYR C 105 PHE 0.012 0.001 PHE C 514 TRP 0.014 0.001 TRP C 183 HIS 0.005 0.001 HIS D1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (29596) covalent geometry : angle 0.61437 / 0.32 (40640) hydrogen bonds : bond 0.04240 / 4.26 ( 1213) hydrogen bonds : angle 4.57003 / 5.95 ( 3360) metal coordination : bond 0.00144 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 235 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASP cc_start: 0.7653 (p0) cc_final: 0.7341 (p0) REVERT: C 83 GLN cc_start: 0.8678 (mp10) cc_final: 0.8239 (mp10) REVERT: C 434 ASP cc_start: 0.8932 (m-30) cc_final: 0.8712 (m-30) REVERT: C 488 MET cc_start: 0.7581 (mmt) cc_final: 0.6901 (mmm) REVERT: C 493 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.6768 (tt) REVERT: C 618 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8474 (tp40) REVERT: C 796 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8490 (pp) REVERT: C 1085 MET cc_start: 0.9456 (mmm) cc_final: 0.9190 (mmm) REVERT: C 1265 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8306 (t80) REVERT: D 237 MET cc_start: 0.9391 (tpp) cc_final: 0.9089 (tpp) REVERT: D 248 ASP cc_start: 0.8998 (m-30) cc_final: 0.8661 (m-30) REVERT: D 264 ASP cc_start: 0.8399 (p0) cc_final: 0.7891 (p0) REVERT: D 298 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8493 (mpp) REVERT: D 304 ASP cc_start: 0.8597 (m-30) cc_final: 0.8261 (m-30) REVERT: D 329 ASP cc_start: 0.8213 (t70) cc_final: 0.7974 (t0) REVERT: D 330 MET cc_start: 0.8348 (ppp) cc_final: 0.7999 (ppp) REVERT: D 826 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7269 (pt) REVERT: D 1249 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8714 (t0) REVERT: E 62 GLN cc_start: 0.8738 (tp40) cc_final: 0.8472 (tp40) REVERT: E 65 ASP cc_start: 0.8996 (m-30) cc_final: 0.8723 (m-30) REVERT: M 365 MET cc_start: 0.5444 (tpp) cc_final: 0.5051 (tpp) REVERT: M 376 MET cc_start: 0.2286 (tpt) cc_final: 0.2049 (tpt) outliers start: 102 outliers final: 40 residues processed: 312 average time/residue: 0.1401 time to fit residues: 73.5986 Evaluate side-chains 258 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 391 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 121 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 368 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 289 optimal weight: 40.0000 chunk 240 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 320 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056486 restraints weight = 98267.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058433 restraints weight = 45630.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059649 restraints weight = 28765.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.060379 restraints weight = 21932.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060790 restraints weight = 18923.219| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29599 Z= 0.191 Angle : 0.601 9.899 40640 Z= 0.315 Chirality : 0.042 0.338 4823 Planarity : 0.004 0.101 4964 Dihedral : 16.386 177.840 5079 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 4.14 % Allowed : 25.37 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3609 helix: 1.20 (0.15), residues: 1302 sheet: 0.08 (0.26), residues: 394 loop : -1.46 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 184 TYR 0.019 0.001 TYR A 185 PHE 0.011 0.001 PHE C 514 TRP 0.020 0.001 TRP D 115 HIS 0.006 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (29596) covalent geometry : angle 0.60070 / 0.31 (40640) hydrogen bonds : bond 0.03988 / 4.05 ( 1213) hydrogen bonds : angle 4.35173 / 5.63 ( 3360) metal coordination : bond 0.00188 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 220 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 201 ARG cc_start: 0.6941 (mmt180) cc_final: 0.6735 (ttp80) REVERT: C 618 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8582 (tp40) REVERT: C 796 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8610 (pp) REVERT: C 936 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7415 (tpp80) REVERT: C 1009 ASN cc_start: 0.8767 (t0) cc_final: 0.8334 (m-40) REVERT: C 1085 MET cc_start: 0.9510 (mmm) cc_final: 0.9207 (mmm) REVERT: C 1265 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8353 (t80) REVERT: C 1329 GLU cc_start: 0.8674 (mt-10) cc_final: 0.7917 (mt-10) REVERT: C 1332 SER cc_start: 0.9667 (OUTLIER) cc_final: 0.9418 (p) REVERT: D 37 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: D 248 ASP cc_start: 0.9007 (m-30) cc_final: 0.8646 (m-30) REVERT: D 264 ASP cc_start: 0.8697 (p0) cc_final: 0.8156 (p0) REVERT: D 267 ASP cc_start: 0.8822 (m-30) cc_final: 0.8453 (m-30) REVERT: D 298 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7958 (mpp) REVERT: D 329 ASP cc_start: 0.8308 (t70) cc_final: 0.8060 (t0) REVERT: D 330 MET cc_start: 0.8452 (ppp) cc_final: 0.7896 (ppp) REVERT: D 826 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7375 (pt) REVERT: D 960 LEU cc_start: 0.8509 (tp) cc_final: 0.8071 (mp) REVERT: E 15 ASN cc_start: 0.8094 (t0) cc_final: 0.7762 (t0) REVERT: E 62 GLN cc_start: 0.8852 (tp40) cc_final: 0.8602 (tp40) REVERT: E 71 GLU cc_start: 0.8693 (mp0) cc_final: 0.8408 (mp0) REVERT: M 365 MET cc_start: 0.5413 (tpp) cc_final: 0.5126 (tpp) REVERT: M 376 MET cc_start: 0.2319 (tpt) cc_final: 0.2078 (tpt) REVERT: M 460 LYS cc_start: 0.6773 (ttpt) cc_final: 0.6567 (pttt) outliers start: 111 outliers final: 63 residues processed: 311 average time/residue: 0.1549 time to fit residues: 79.7850 Evaluate side-chains 280 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 209 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 245 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 263 optimal weight: 0.9990 chunk 281 optimal weight: 20.0000 chunk 189 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 288 optimal weight: 0.0370 chunk 261 optimal weight: 5.9990 chunk 345 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1220 GLN M 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.088371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.057292 restraints weight = 96997.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059272 restraints weight = 45142.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.060503 restraints weight = 28404.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.061231 restraints weight = 21688.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.061629 restraints weight = 18683.471| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29599 Z= 0.125 Angle : 0.571 9.968 40640 Z= 0.296 Chirality : 0.042 0.347 4823 Planarity : 0.004 0.081 4964 Dihedral : 16.349 177.555 5076 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 3.69 % Allowed : 25.86 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3609 helix: 1.29 (0.15), residues: 1308 sheet: 0.07 (0.26), residues: 385 loop : -1.44 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 69 TYR 0.019 0.001 TYR A 185 PHE 0.009 0.001 PHE M 397 TRP 0.009 0.001 TRP D 115 HIS 0.004 0.001 HIS D1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29596) covalent geometry : angle 0.57121 / 0.30 (40640) hydrogen bonds : bond 0.03554 / 3.62 ( 1213) hydrogen bonds : angle 4.15871 / 5.36 ( 3360) metal coordination : bond 0.00135 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 222 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.8860 (tt0) cc_final: 0.8587 (tt0) REVERT: C 81 ASP cc_start: 0.7956 (p0) cc_final: 0.7444 (p0) REVERT: C 83 GLN cc_start: 0.8900 (mp10) cc_final: 0.8214 (mp10) REVERT: C 479 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8421 (tp) REVERT: C 618 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8333 (tp40) REVERT: C 796 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8588 (pp) REVERT: C 954 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9304 (ptpp) REVERT: C 1085 MET cc_start: 0.9489 (mmm) cc_final: 0.9042 (mmm) REVERT: C 1329 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 37 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: D 237 MET cc_start: 0.9393 (tpp) cc_final: 0.9094 (tpp) REVERT: D 248 ASP cc_start: 0.9000 (m-30) cc_final: 0.8625 (m-30) REVERT: D 264 ASP cc_start: 0.8615 (p0) cc_final: 0.7946 (p0) REVERT: D 267 ASP cc_start: 0.8776 (m-30) cc_final: 0.8231 (m-30) REVERT: D 298 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: D 329 ASP cc_start: 0.8299 (t70) cc_final: 0.8024 (t0) REVERT: D 330 MET cc_start: 0.8363 (ppp) cc_final: 0.7754 (ppp) REVERT: D 402 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 770 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9039 (mm) REVERT: E 15 ASN cc_start: 0.7821 (t0) cc_final: 0.7617 (t0) REVERT: E 62 GLN cc_start: 0.8877 (tp40) cc_final: 0.8605 (tp40) REVERT: E 65 ASP cc_start: 0.9209 (m-30) cc_final: 0.8826 (m-30) REVERT: E 71 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: M 156 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8977 (tp) REVERT: M 365 MET cc_start: 0.5370 (tpp) cc_final: 0.5089 (tpp) REVERT: M 376 MET cc_start: 0.2135 (tpt) cc_final: 0.1762 (tpt) REVERT: M 408 ASN cc_start: -0.0191 (OUTLIER) cc_final: -0.0428 (p0) REVERT: M 460 LYS cc_start: 0.6830 (ttpt) cc_final: 0.6054 (ptpt) outliers start: 99 outliers final: 58 residues processed: 300 average time/residue: 0.1669 time to fit residues: 84.2872 Evaluate side-chains 277 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Chi-restraints excluded: chain M residue 408 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 257 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 176 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057842 restraints weight = 97457.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.059823 restraints weight = 45282.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061077 restraints weight = 28418.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061824 restraints weight = 21644.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.062120 restraints weight = 18609.769| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29599 Z= 0.109 Angle : 0.556 11.135 40640 Z= 0.288 Chirality : 0.041 0.351 4823 Planarity : 0.004 0.107 4964 Dihedral : 16.311 178.063 5076 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 3.61 % Allowed : 26.34 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3609 helix: 1.41 (0.15), residues: 1299 sheet: 0.11 (0.26), residues: 385 loop : -1.39 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.019 0.001 TYR A 185 PHE 0.009 0.001 PHE M 397 TRP 0.014 0.001 TRP M 212 HIS 0.004 0.001 HIS D1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (29596) covalent geometry : angle 0.55650 / 0.29 (40640) hydrogen bonds : bond 0.03336 / 3.40 ( 1213) hydrogen bonds : angle 4.03912 / 5.20 ( 3360) metal coordination : bond 0.00072 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 224 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLN cc_start: 0.8849 (tt0) cc_final: 0.8566 (tt0) REVERT: C 81 ASP cc_start: 0.7925 (p0) cc_final: 0.7583 (p0) REVERT: C 83 GLN cc_start: 0.8960 (mp10) cc_final: 0.8179 (mp10) REVERT: C 479 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8368 (tp) REVERT: C 492 MET cc_start: 0.7755 (ppp) cc_final: 0.7543 (ppp) REVERT: C 493 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.6682 (tt) REVERT: C 538 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9054 (pp) REVERT: C 796 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8259 (pp) REVERT: C 936 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7605 (ttm-80) REVERT: C 954 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9298 (ptpp) REVERT: C 1009 ASN cc_start: 0.8739 (t0) cc_final: 0.8287 (m110) REVERT: C 1085 MET cc_start: 0.9464 (mmm) cc_final: 0.8979 (mmm) REVERT: C 1119 MET cc_start: 0.8646 (ttt) cc_final: 0.8293 (ttp) REVERT: C 1233 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8955 (mt) REVERT: C 1329 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7674 (mt-10) REVERT: C 1332 SER cc_start: 0.9609 (OUTLIER) cc_final: 0.9406 (p) REVERT: D 248 ASP cc_start: 0.8992 (m-30) cc_final: 0.8608 (m-30) REVERT: D 264 ASP cc_start: 0.8617 (p0) cc_final: 0.8072 (p0) REVERT: D 267 ASP cc_start: 0.8691 (m-30) cc_final: 0.8265 (m-30) REVERT: D 298 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.7932 (mpp) REVERT: D 329 ASP cc_start: 0.8291 (t70) cc_final: 0.7993 (t0) REVERT: D 330 MET cc_start: 0.8316 (ppp) cc_final: 0.7714 (ppp) REVERT: D 826 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7290 (pt) REVERT: D 960 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7899 (mt) REVERT: E 62 GLN cc_start: 0.8865 (tp40) cc_final: 0.8597 (tp40) REVERT: E 67 ARG cc_start: 0.9161 (tpp80) cc_final: 0.8763 (tpp80) REVERT: E 71 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: M 156 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8963 (tp) REVERT: M 365 MET cc_start: 0.5306 (tpp) cc_final: 0.5096 (tpp) REVERT: M 376 MET cc_start: 0.2146 (tpt) cc_final: 0.1889 (tpt) REVERT: M 460 LYS cc_start: 0.6851 (ttpt) cc_final: 0.6028 (ptpt) outliers start: 97 outliers final: 63 residues processed: 301 average time/residue: 0.1729 time to fit residues: 87.2816 Evaluate side-chains 282 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 206 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 74 optimal weight: 5.9990 chunk 302 optimal weight: 50.0000 chunk 142 optimal weight: 0.0570 chunk 172 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 208 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.086502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055642 restraints weight = 97279.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.057555 restraints weight = 45441.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058746 restraints weight = 28720.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059428 restraints weight = 21931.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059848 restraints weight = 18956.026| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29599 Z= 0.196 Angle : 0.594 9.523 40640 Z= 0.308 Chirality : 0.042 0.316 4823 Planarity : 0.004 0.089 4964 Dihedral : 16.329 177.956 5076 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.77 % Rotamer: Outliers : 4.43 % Allowed : 25.89 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3609 helix: 1.40 (0.15), residues: 1310 sheet: 0.16 (0.27), residues: 384 loop : -1.39 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.018 0.001 TYR A 185 PHE 0.012 0.001 PHE C1323 TRP 0.020 0.001 TRP M 212 HIS 0.004 0.001 HIS D1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (29596) covalent geometry : angle 0.59432 / 0.31 (40640) hydrogen bonds : bond 0.03588 / 3.65 ( 1213) hydrogen bonds : angle 4.06318 / 5.22 ( 3360) metal coordination : bond 0.00153 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 205 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 283 GLN cc_start: 0.8937 (tt0) cc_final: 0.8670 (tt0) REVERT: B 194 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: C 83 GLN cc_start: 0.9025 (mp10) cc_final: 0.8546 (mp10) REVERT: C 538 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9057 (pp) REVERT: C 796 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8496 (pp) REVERT: C 936 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7781 (tpp80) REVERT: C 954 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9320 (ptpp) REVERT: C 1009 ASN cc_start: 0.8863 (t0) cc_final: 0.8607 (m110) REVERT: C 1085 MET cc_start: 0.9522 (mmm) cc_final: 0.9034 (mmm) REVERT: C 1119 MET cc_start: 0.8680 (ttt) cc_final: 0.8446 (ttp) REVERT: C 1265 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8314 (t80) REVERT: C 1329 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 248 ASP cc_start: 0.8997 (m-30) cc_final: 0.8565 (m-30) REVERT: D 264 ASP cc_start: 0.8661 (p0) cc_final: 0.8076 (p0) REVERT: D 267 ASP cc_start: 0.8702 (m-30) cc_final: 0.8274 (m-30) REVERT: D 298 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.7849 (mpp) REVERT: D 329 ASP cc_start: 0.8395 (t70) cc_final: 0.8111 (t0) REVERT: D 330 MET cc_start: 0.8304 (ppp) cc_final: 0.7673 (ppp) REVERT: D 484 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8424 (mtm) REVERT: D 558 ASP cc_start: 0.6873 (p0) cc_final: 0.6615 (p0) REVERT: D 826 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7429 (pt) REVERT: D 833 GLU cc_start: 0.8704 (tp30) cc_final: 0.8499 (tp30) REVERT: D 1366 HIS cc_start: 0.9406 (OUTLIER) cc_final: 0.9135 (m170) REVERT: E 62 GLN cc_start: 0.8957 (tp40) cc_final: 0.8665 (tp40) REVERT: E 65 ASP cc_start: 0.9207 (m-30) cc_final: 0.8954 (m-30) REVERT: E 67 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8773 (tpp80) REVERT: E 71 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: M 156 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8974 (tp) REVERT: M 376 MET cc_start: 0.2181 (tpt) cc_final: 0.1900 (tpt) REVERT: M 460 LYS cc_start: 0.6813 (ttpt) cc_final: 0.5969 (ptpt) outliers start: 119 outliers final: 80 residues processed: 304 average time/residue: 0.1685 time to fit residues: 85.7960 Evaluate side-chains 294 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 201 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 282 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 686 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.054450 restraints weight = 97288.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056327 restraints weight = 45481.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.057490 restraints weight = 28775.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058193 restraints weight = 22035.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058512 restraints weight = 18975.867| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29599 Z= 0.226 Angle : 0.620 10.307 40640 Z= 0.321 Chirality : 0.043 0.464 4823 Planarity : 0.004 0.088 4964 Dihedral : 16.387 177.508 5076 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.87 % Favored : 94.10 % Rotamer: Outliers : 4.81 % Allowed : 25.71 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3609 helix: 1.38 (0.15), residues: 1315 sheet: 0.03 (0.26), residues: 383 loop : -1.40 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 421 TYR 0.024 0.001 TYR A 185 PHE 0.012 0.001 PHE C1323 TRP 0.015 0.001 TRP M 212 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (29596) covalent geometry : angle 0.62011 / 0.32 (40640) hydrogen bonds : bond 0.03624 / 3.72 ( 1213) hydrogen bonds : angle 4.08143 / 5.23 ( 3360) metal coordination : bond 0.00286 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 202 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 283 GLN cc_start: 0.9032 (tt0) cc_final: 0.8794 (tt0) REVERT: B 194 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: C 81 ASP cc_start: 0.7918 (p0) cc_final: 0.7710 (p0) REVERT: C 83 GLN cc_start: 0.8955 (mp10) cc_final: 0.8339 (pm20) REVERT: C 479 LEU cc_start: 0.9185 (mm) cc_final: 0.8466 (tp) REVERT: C 493 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7067 (tt) REVERT: C 538 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9071 (pp) REVERT: C 618 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7705 (tp40) REVERT: C 653 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.7807 (tpt) REVERT: C 796 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.8829 (pp) REVERT: C 936 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7913 (tpp80) REVERT: C 1085 MET cc_start: 0.9542 (mmm) cc_final: 0.9135 (mmm) REVERT: C 1119 MET cc_start: 0.8684 (ttt) cc_final: 0.8456 (ttp) REVERT: C 1265 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8287 (t80) REVERT: C 1329 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7560 (mt-10) REVERT: D 37 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7339 (tp30) REVERT: D 248 ASP cc_start: 0.9018 (m-30) cc_final: 0.8679 (m-30) REVERT: D 264 ASP cc_start: 0.8683 (p0) cc_final: 0.8040 (p0) REVERT: D 267 ASP cc_start: 0.8688 (m-30) cc_final: 0.8216 (m-30) REVERT: D 298 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.7922 (mpp) REVERT: D 329 ASP cc_start: 0.8445 (t70) cc_final: 0.8169 (t0) REVERT: D 330 MET cc_start: 0.8350 (ppp) cc_final: 0.7692 (ppp) REVERT: D 478 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9308 (mm) REVERT: D 484 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8381 (mtm) REVERT: D 960 LEU cc_start: 0.8307 (tp) cc_final: 0.8004 (mt) REVERT: D 1366 HIS cc_start: 0.9423 (OUTLIER) cc_final: 0.9163 (m170) REVERT: E 62 GLN cc_start: 0.9001 (tp40) cc_final: 0.8741 (tp40) REVERT: E 67 ARG cc_start: 0.9169 (tpp80) cc_final: 0.8800 (tpp80) REVERT: E 71 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: M 156 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8964 (tp) REVERT: M 376 MET cc_start: 0.2353 (tpt) cc_final: 0.2092 (tpt) REVERT: M 460 LYS cc_start: 0.6848 (ttpt) cc_final: 0.6031 (ptpt) outliers start: 129 outliers final: 80 residues processed: 311 average time/residue: 0.1639 time to fit residues: 85.2530 Evaluate side-chains 292 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 196 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 96 optimal weight: 8.9990 chunk 325 optimal weight: 0.1980 chunk 223 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 159 optimal weight: 7.9990 chunk 314 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 349 optimal weight: 40.0000 chunk 252 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 266 ASN D 560 ASN D1023 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.084847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.054002 restraints weight = 97807.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055891 restraints weight = 45497.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057061 restraints weight = 28698.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057745 restraints weight = 21943.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058130 restraints weight = 18944.470| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29599 Z= 0.215 Angle : 0.622 9.795 40640 Z= 0.321 Chirality : 0.043 0.288 4823 Planarity : 0.004 0.082 4964 Dihedral : 16.402 177.335 5076 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.65 % Rotamer: Outliers : 4.55 % Allowed : 25.86 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3609 helix: 1.38 (0.15), residues: 1316 sheet: 0.01 (0.26), residues: 381 loop : -1.40 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.018 0.001 TYR A 185 PHE 0.011 0.001 PHE C 514 TRP 0.013 0.001 TRP D 115 HIS 0.004 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (29596) covalent geometry : angle 0.62217 / 0.32 (40640) hydrogen bonds : bond 0.03604 / 3.70 ( 1213) hydrogen bonds : angle 4.06147 / 5.20 ( 3360) metal coordination : bond 0.00261 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 203 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 283 GLN cc_start: 0.9052 (tt0) cc_final: 0.8815 (tt0) REVERT: A 291 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8848 (mtmm) REVERT: C 81 ASP cc_start: 0.8075 (p0) cc_final: 0.7791 (p0) REVERT: C 83 GLN cc_start: 0.8962 (mp10) cc_final: 0.8411 (mp10) REVERT: C 188 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7738 (m-10) REVERT: C 493 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7244 (tt) REVERT: C 538 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9017 (pp) REVERT: C 542 ARG cc_start: 0.8158 (mmp80) cc_final: 0.7465 (mtt90) REVERT: C 796 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8636 (pp) REVERT: C 936 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7908 (tpp80) REVERT: C 1042 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8317 (tp) REVERT: C 1085 MET cc_start: 0.9554 (mmm) cc_final: 0.9183 (mmm) REVERT: C 1119 MET cc_start: 0.8683 (ttt) cc_final: 0.8463 (ttp) REVERT: C 1329 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7617 (mt-10) REVERT: D 37 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: D 248 ASP cc_start: 0.9026 (m-30) cc_final: 0.8654 (m-30) REVERT: D 264 ASP cc_start: 0.8655 (p0) cc_final: 0.8026 (p0) REVERT: D 267 ASP cc_start: 0.8680 (m-30) cc_final: 0.8201 (m-30) REVERT: D 329 ASP cc_start: 0.8510 (t70) cc_final: 0.8247 (t0) REVERT: D 330 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7787 (ppp) REVERT: D 340 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7048 (mm-40) REVERT: D 478 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9302 (mm) REVERT: D 484 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8396 (mtm) REVERT: D 960 LEU cc_start: 0.8332 (tp) cc_final: 0.8012 (mt) REVERT: D 1366 HIS cc_start: 0.9420 (OUTLIER) cc_final: 0.9138 (m170) REVERT: E 62 GLN cc_start: 0.9077 (tp40) cc_final: 0.8839 (tp40) REVERT: E 67 ARG cc_start: 0.9169 (tpp80) cc_final: 0.8831 (tpp80) REVERT: E 71 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: M 156 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8961 (tp) REVERT: M 460 LYS cc_start: 0.6719 (ttpt) cc_final: 0.5926 (ptpt) outliers start: 122 outliers final: 88 residues processed: 304 average time/residue: 0.1721 time to fit residues: 87.5555 Evaluate side-chains 301 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 199 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 217 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 280 optimal weight: 20.0000 chunk 297 optimal weight: 50.0000 chunk 322 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.085136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.054344 restraints weight = 97060.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056220 restraints weight = 45134.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.057385 restraints weight = 28557.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.058061 restraints weight = 21843.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058469 restraints weight = 18851.999| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29599 Z= 0.173 Angle : 0.615 13.445 40640 Z= 0.314 Chirality : 0.043 0.474 4823 Planarity : 0.004 0.079 4964 Dihedral : 16.402 177.696 5076 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.99 % Rotamer: Outliers : 3.87 % Allowed : 26.60 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3609 helix: 1.41 (0.15), residues: 1318 sheet: 0.02 (0.26), residues: 375 loop : -1.39 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 436 TYR 0.019 0.001 TYR A 185 PHE 0.012 0.001 PHE C1323 TRP 0.012 0.001 TRP M 212 HIS 0.021 0.001 HIS D1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (29596) covalent geometry : angle 0.61532 / 0.31 (40640) hydrogen bonds : bond 0.03482 / 3.58 ( 1213) hydrogen bonds : angle 4.02081 / 5.14 ( 3360) metal coordination : bond 0.00218 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 209 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 194 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: C 81 ASP cc_start: 0.8008 (p0) cc_final: 0.7805 (p0) REVERT: C 83 GLN cc_start: 0.8989 (mp10) cc_final: 0.8437 (mp10) REVERT: C 479 LEU cc_start: 0.9190 (mm) cc_final: 0.8478 (tp) REVERT: C 538 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9054 (pp) REVERT: C 542 ARG cc_start: 0.8156 (mmp80) cc_final: 0.7393 (ttt90) REVERT: C 549 ASP cc_start: 0.8755 (m-30) cc_final: 0.8448 (m-30) REVERT: C 653 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.7795 (tpt) REVERT: C 796 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8680 (pp) REVERT: C 936 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7968 (tpp80) REVERT: C 1041 ASP cc_start: 0.8498 (t0) cc_final: 0.8209 (p0) REVERT: C 1085 MET cc_start: 0.9538 (mmm) cc_final: 0.9126 (mmm) REVERT: C 1119 MET cc_start: 0.8660 (ttt) cc_final: 0.8442 (ttp) REVERT: C 1329 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7568 (mt-10) REVERT: D 37 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: D 115 TRP cc_start: 0.8932 (OUTLIER) cc_final: 0.7836 (m-90) REVERT: D 248 ASP cc_start: 0.9025 (m-30) cc_final: 0.8658 (m-30) REVERT: D 264 ASP cc_start: 0.8651 (p0) cc_final: 0.8017 (p0) REVERT: D 267 ASP cc_start: 0.8629 (m-30) cc_final: 0.8153 (m-30) REVERT: D 329 ASP cc_start: 0.8473 (t70) cc_final: 0.8198 (t0) REVERT: D 330 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7750 (ppp) REVERT: D 340 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7042 (mm-40) REVERT: D 484 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8340 (mtm) REVERT: D 802 ASP cc_start: 0.8842 (t70) cc_final: 0.8616 (t0) REVERT: D 960 LEU cc_start: 0.8308 (tp) cc_final: 0.7962 (mt) REVERT: D 1366 HIS cc_start: 0.9410 (OUTLIER) cc_final: 0.9121 (m170) REVERT: E 62 GLN cc_start: 0.9023 (tp40) cc_final: 0.8782 (tp40) REVERT: E 67 ARG cc_start: 0.9179 (tpp80) cc_final: 0.8816 (tpp80) REVERT: E 71 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: M 156 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8947 (tp) REVERT: M 460 LYS cc_start: 0.6709 (ttpt) cc_final: 0.5918 (ptpt) outliers start: 104 outliers final: 85 residues processed: 293 average time/residue: 0.1688 time to fit residues: 82.5836 Evaluate side-chains 299 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 201 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 288 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 278 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 350 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 560 ASN D1023 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055114 restraints weight = 96883.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.057026 restraints weight = 44836.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.058207 restraints weight = 28197.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058907 restraints weight = 21561.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059278 restraints weight = 18596.714| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29599 Z= 0.133 Angle : 0.601 13.580 40640 Z= 0.306 Chirality : 0.043 0.423 4823 Planarity : 0.004 0.075 4964 Dihedral : 16.361 178.756 5076 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 3.28 % Allowed : 27.16 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3609 helix: 1.44 (0.15), residues: 1322 sheet: 0.06 (0.26), residues: 382 loop : -1.36 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 69 TYR 0.018 0.001 TYR A 185 PHE 0.010 0.001 PHE M 397 TRP 0.014 0.001 TRP M 212 HIS 0.003 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (29596) covalent geometry : angle 0.60140 / 0.31 (40640) hydrogen bonds : bond 0.03296 / 3.39 ( 1213) hydrogen bonds : angle 3.97084 / 5.07 ( 3360) metal coordination : bond 0.00170 / 0.17 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 207 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8201 (mmm) cc_final: 0.7983 (tpp) REVERT: A 262 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8307 (tp) REVERT: A 283 GLN cc_start: 0.9184 (tt0) cc_final: 0.8967 (tp40) REVERT: B 194 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: C 81 ASP cc_start: 0.7991 (p0) cc_final: 0.7788 (p0) REVERT: C 83 GLN cc_start: 0.8966 (mp10) cc_final: 0.8417 (mp10) REVERT: C 188 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7427 (m-10) REVERT: C 493 ILE cc_start: 0.7752 (pt) cc_final: 0.7183 (tt) REVERT: C 538 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9058 (pp) REVERT: C 542 ARG cc_start: 0.8138 (mmp80) cc_final: 0.7450 (ttt90) REVERT: C 549 ASP cc_start: 0.8719 (m-30) cc_final: 0.8437 (m-30) REVERT: C 653 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.7857 (tpt) REVERT: C 796 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8589 (pp) REVERT: C 930 ASP cc_start: 0.7957 (t0) cc_final: 0.7740 (t0) REVERT: C 936 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7890 (tpp80) REVERT: C 1041 ASP cc_start: 0.8453 (t0) cc_final: 0.8115 (p0) REVERT: C 1085 MET cc_start: 0.9506 (mmm) cc_final: 0.9063 (mmm) REVERT: C 1119 MET cc_start: 0.8616 (ttt) cc_final: 0.8397 (ttp) REVERT: C 1329 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 37 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: D 248 ASP cc_start: 0.8984 (m-30) cc_final: 0.8656 (m-30) REVERT: D 264 ASP cc_start: 0.8576 (p0) cc_final: 0.7952 (p0) REVERT: D 267 ASP cc_start: 0.8626 (m-30) cc_final: 0.8140 (m-30) REVERT: D 329 ASP cc_start: 0.8405 (t70) cc_final: 0.8136 (t0) REVERT: D 330 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7810 (ppp) REVERT: D 340 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7014 (mm-40) REVERT: D 484 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8576 (mmm) REVERT: D 802 ASP cc_start: 0.8787 (t70) cc_final: 0.8543 (t0) REVERT: D 960 LEU cc_start: 0.8246 (tp) cc_final: 0.7886 (mt) REVERT: D 1366 HIS cc_start: 0.9380 (OUTLIER) cc_final: 0.9044 (m170) REVERT: E 41 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7811 (tm-30) REVERT: E 62 GLN cc_start: 0.9001 (tp40) cc_final: 0.8771 (tp40) REVERT: E 67 ARG cc_start: 0.9169 (tpp80) cc_final: 0.8827 (tpp80) REVERT: E 71 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: M 156 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8956 (tp) REVERT: M 460 LYS cc_start: 0.6722 (ttpt) cc_final: 0.5936 (ptpt) outliers start: 88 outliers final: 68 residues processed: 278 average time/residue: 0.1780 time to fit residues: 82.2073 Evaluate side-chains 284 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 203 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 231 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 301 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 560 ASN D1259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.053157 restraints weight = 98479.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054999 restraints weight = 46711.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056144 restraints weight = 29904.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.056805 restraints weight = 23093.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.057198 restraints weight = 20036.175| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29599 Z= 0.237 Angle : 0.649 12.560 40640 Z= 0.332 Chirality : 0.044 0.442 4823 Planarity : 0.004 0.080 4964 Dihedral : 16.391 178.386 5076 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.37 % Favored : 93.60 % Rotamer: Outliers : 3.32 % Allowed : 27.12 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3609 helix: 1.41 (0.15), residues: 1321 sheet: -0.02 (0.26), residues: 381 loop : -1.39 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 69 TYR 0.019 0.001 TYR A 185 PHE 0.014 0.001 PHE C1323 TRP 0.014 0.001 TRP D 115 HIS 0.004 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (29596) covalent geometry : angle 0.64909 / 0.33 (40640) hydrogen bonds : bond 0.03680 / 3.77 ( 1213) hydrogen bonds : angle 4.07206 / 5.18 ( 3360) metal coordination : bond 0.00225 / 0.22 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5632.03 seconds wall clock time: 97 minutes 34.04 seconds (5854.04 seconds total)