Starting phenix.real_space_refine on Tue Jun 24 16:33:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rec_19082/06_2025/8rec_19082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rec_19082/06_2025/8rec_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_19082/06_2025/8rec_19082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rec_19082/06_2025/8rec_19082.map" model { file = "/net/cci-nas-00/data/ceres_data/8rec_19082/06_2025/8rec_19082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rec_19082/06_2025/8rec_19082.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 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: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} 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, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} 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, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 31, 'ARG:plan': 19} 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: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} 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: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 12, 'ASP:plan': 12} 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: 19.98, per 1000 atoms: 0.69 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: 9.81 Conformation dependent library (CDL) restraints added in 3.8 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: 13.53 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: 23.29 Time building geometry restraints manager: 10.82 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=" N PRO M 211 " pdb=" CA PRO M 211 " ideal model delta sigma weight residual 1.469 1.419 0.050 1.25e-02 6.40e+03 1.58e+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: 16872 35.43 - 70.86: 874 70.86 - 106.28: 38 106.28 - 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=" 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 dihedral pdb=" C4' DT N 2 " pdb=" C3' DT N 2 " pdb=" O3' DT N 2 " pdb=" P DA N 3 " ideal model delta sinusoidal sigma weight residual -140.00 19.65 -159.65 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 17783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4243 0.064 - 0.128: 557 0.128 - 0.191: 19 0.191 - 0.255: 3 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=" CG LEU C 845 " pdb=" CB LEU C 845 " pdb=" CD1 LEU C 845 " pdb=" CD2 LEU C 845 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1' G R -1 " pdb=" O4' G R -1 " pdb=" C2' G R -1 " pdb=" N9 G R -1 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.06e+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: 0.000 Normalize map: mean=0, sd=1: 39.150 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: 0.080 Extract box with map and model: 1.760 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 96.980 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:4.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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= 0.164 Angle : 0.766 73.826 40640 Z= 0.383 Chirality : 0.042 0.319 4823 Planarity : 0.005 0.125 4964 Dihedral : 19.110 177.140 11044 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), 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 TRP 0.011 0.001 TRP C 183 HIS 0.012 0.001 HIS M 391 PHE 0.014 0.001 PHE A 231 TYR 0.017 0.001 TYR A 185 ARG 0.008 0.000 ARG D1140 Details of bonding type rmsd hydrogen bonds : bond 0.15646 ( 1213) hydrogen bonds : angle 5.78146 ( 3360) metal coordination : bond 0.00070 ( 3) covalent geometry : bond 0.00481 (29596) covalent geometry : angle 0.76603 (40640) *********************** 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 : 3.342 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: 0.6153 (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: 0.4701 time to fit residues: 248.7418 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 : 2.886 ------------------------------------------------------------------------------- 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 312 optimal weight: 20.0000 chunk 280 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 chunk 189 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 chunk 290 optimal weight: 50.0000 chunk 112 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 336 optimal weight: 50.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3645 r_free = 0.3645 target = 0.089148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.058160 restraints weight = 97019.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.060145 restraints weight = 45166.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061383 restraints weight = 28414.440| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 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 = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29599 Z= 0.146 Angle : 0.594 10.201 40640 Z= 0.308 Chirality : 0.041 0.207 4823 Planarity : 0.005 0.076 4964 Dihedral : 16.314 176.413 5086 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 4.14 % Allowed : 25.60 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3609 helix: 1.13 (0.15), residues: 1299 sheet: 0.10 (0.26), residues: 384 loop : -1.42 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 183 HIS 0.004 0.001 HIS C1070 PHE 0.012 0.001 PHE C 514 TYR 0.027 0.001 TYR C 105 ARG 0.007 0.001 ARG D 259 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1213) hydrogen bonds : angle 4.41722 ( 3360) metal coordination : bond 0.00102 ( 3) covalent geometry : bond 0.00331 (29596) covalent geometry : angle 0.59403 (40640) *********************** 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 353 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 242 time to evaluate : 3.413 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: 0.7774 (p0) cc_final: 0.7469 (p0) REVERT: C 83 GLN cc_start: 0.8769 (mp10) cc_final: 0.8340 (mp10) REVERT: C 434 ASP cc_start: 0.8952 (m-30) cc_final: 0.8738 (m-30) REVERT: C 493 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7001 (tt) REVERT: C 618 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8541 (tp40) REVERT: C 796 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8538 (pp) REVERT: C 1085 MET cc_start: 0.9465 (mmm) cc_final: 0.9187 (mmm) REVERT: C 1265 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8319 (t80) REVERT: D 37 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: D 237 MET cc_start: 0.9428 (tpp) cc_final: 0.9100 (tpp) REVERT: D 248 ASP cc_start: 0.8984 (m-30) cc_final: 0.8666 (m-30) REVERT: D 264 ASP cc_start: 0.8489 (p0) cc_final: 0.7960 (p0) REVERT: D 298 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8457 (mpp) REVERT: D 304 ASP cc_start: 0.8621 (m-30) cc_final: 0.8287 (m-30) REVERT: D 330 MET cc_start: 0.8321 (ppp) cc_final: 0.7949 (ppp) REVERT: D 1249 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8711 (t0) REVERT: E 15 ASN cc_start: 0.7827 (t0) cc_final: 0.7475 (t0) REVERT: E 62 GLN cc_start: 0.8786 (tp40) cc_final: 0.8548 (tp40) REVERT: M 365 MET cc_start: 0.5324 (tpp) cc_final: 0.4979 (tpp) REVERT: M 376 MET cc_start: 0.2210 (tpt) cc_final: 0.1972 (tpt) REVERT: M 460 LYS cc_start: 0.6877 (pttm) cc_final: 0.6354 (ptpt) outliers start: 111 outliers final: 49 residues processed: 327 average time/residue: 0.5802 time to fit residues: 319.1482 Evaluate side-chains 268 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 2.925 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 282 VAL 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 356 THR 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 841 ARG 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 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 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 975 ILE 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 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 391 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 321 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 160 optimal weight: 50.0000 chunk 276 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 311 optimal weight: 30.0000 chunk 304 optimal weight: 0.4980 chunk 349 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.087903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.057062 restraints weight = 97210.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059024 restraints weight = 45073.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.060228 restraints weight = 28299.914| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29599 Z= 0.158 Angle : 0.567 9.463 40640 Z= 0.294 Chirality : 0.041 0.205 4823 Planarity : 0.004 0.057 4964 Dihedral : 16.267 176.894 5078 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer: Outliers : 4.02 % Allowed : 25.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3609 helix: 1.29 (0.15), residues: 1298 sheet: 0.10 (0.26), residues: 385 loop : -1.42 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.004 0.001 HIS D1023 PHE 0.011 0.001 PHE C 514 TYR 0.017 0.001 TYR A 185 ARG 0.009 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 1213) hydrogen bonds : angle 4.20319 ( 3360) metal coordination : bond 0.00164 ( 3) covalent geometry : bond 0.00355 (29596) covalent geometry : angle 0.56666 (40640) *********************** 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 336 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 228 time to evaluate : 2.945 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: 0.8774 (tt0) cc_final: 0.8538 (tt0) REVERT: C 81 ASP cc_start: 0.7883 (p0) cc_final: 0.7642 (p0) REVERT: C 83 GLN cc_start: 0.8896 (mp10) cc_final: 0.8455 (mp10) REVERT: C 201 ARG cc_start: 0.6802 (ttp80) cc_final: 0.6259 (mtp-110) REVERT: C 479 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8445 (tp) REVERT: C 493 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.6876 (tt) REVERT: C 618 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8650 (tp40) REVERT: C 796 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8587 (pp) REVERT: C 936 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7459 (tpp80) REVERT: C 1009 ASN cc_start: 0.8818 (t0) cc_final: 0.8333 (m110) REVERT: C 1085 MET cc_start: 0.9494 (mmm) cc_final: 0.9190 (mmm) REVERT: C 1265 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8283 (t80) REVERT: C 1329 GLU cc_start: 0.8619 (mt-10) cc_final: 0.7853 (mt-10) REVERT: D 37 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: D 248 ASP cc_start: 0.9001 (m-30) cc_final: 0.8654 (m-30) REVERT: D 264 ASP cc_start: 0.8706 (p0) cc_final: 0.8128 (p0) REVERT: D 267 ASP cc_start: 0.8707 (m-30) cc_final: 0.8342 (m-30) REVERT: D 298 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.7944 (mpp) REVERT: D 330 MET cc_start: 0.8378 (ppp) cc_final: 0.7770 (ppp) REVERT: D 340 GLN cc_start: 0.7535 (mm-40) cc_final: 0.6851 (mm-40) REVERT: D 1248 ILE cc_start: 0.9321 (mt) cc_final: 0.9099 (tt) REVERT: E 15 ASN cc_start: 0.8106 (t0) cc_final: 0.7577 (t0) REVERT: E 62 GLN cc_start: 0.8903 (tp40) cc_final: 0.8674 (tp40) REVERT: E 71 GLU cc_start: 0.8776 (mp0) cc_final: 0.8398 (mp0) REVERT: M 365 MET cc_start: 0.5336 (tpp) cc_final: 0.5066 (tpp) REVERT: M 376 MET cc_start: 0.2200 (tpt) cc_final: 0.1962 (tpt) REVERT: M 460 LYS cc_start: 0.6835 (pttm) cc_final: 0.6035 (ptpt) outliers start: 108 outliers final: 61 residues processed: 313 average time/residue: 0.3639 time to fit residues: 188.4146 Evaluate side-chains 281 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 2.953 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL 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 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 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 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 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 241 VAL 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 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 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 E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 317 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 332 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 195 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.088299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.057432 restraints weight = 97808.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059421 restraints weight = 45172.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060669 restraints weight = 28257.550| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 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 = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1869 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= 0.124 Angle : 0.550 10.243 40640 Z= 0.283 Chirality : 0.041 0.216 4823 Planarity : 0.004 0.063 4964 Dihedral : 16.192 177.045 5076 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.18 % Rotamer: Outliers : 3.58 % Allowed : 26.30 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3609 helix: 1.37 (0.15), residues: 1297 sheet: 0.13 (0.27), residues: 385 loop : -1.41 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 212 HIS 0.004 0.001 HIS D1023 PHE 0.009 0.001 PHE C 390 TYR 0.019 0.001 TYR A 185 ARG 0.013 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 1213) hydrogen bonds : angle 4.02404 ( 3360) metal coordination : bond 0.00115 ( 3) covalent geometry : bond 0.00274 (29596) covalent geometry : angle 0.54983 (40640) *********************** 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 312 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 216 time to evaluate : 2.916 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: 0.8300 (OUTLIER) cc_final: 0.7884 (tp) REVERT: A 283 GLN cc_start: 0.8864 (tt0) cc_final: 0.8618 (tt0) REVERT: C 81 ASP cc_start: 0.7948 (p0) cc_final: 0.7670 (p0) REVERT: C 83 GLN cc_start: 0.8925 (mp10) cc_final: 0.8468 (mp10) REVERT: C 201 ARG cc_start: 0.6876 (ttp80) cc_final: 0.6480 (mtp-110) REVERT: C 479 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8340 (tp) REVERT: C 538 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9040 (pp) REVERT: C 796 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8540 (pp) REVERT: C 954 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9301 (ptpp) REVERT: C 1085 MET cc_start: 0.9469 (mmm) cc_final: 0.8883 (mmm) REVERT: C 1119 MET cc_start: 0.8636 (ttt) cc_final: 0.8293 (ttp) REVERT: C 1220 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: C 1329 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7790 (mt-10) REVERT: D 37 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7385 (tp30) REVERT: D 248 ASP cc_start: 0.9011 (m-30) cc_final: 0.8696 (m-30) REVERT: D 264 ASP cc_start: 0.8632 (p0) cc_final: 0.8057 (p0) REVERT: D 267 ASP cc_start: 0.8632 (m-30) cc_final: 0.8267 (m-30) REVERT: D 298 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: D 330 MET cc_start: 0.8358 (ppp) cc_final: 0.7810 (ppp) REVERT: D 402 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7812 (tm-30) REVERT: E 15 ASN cc_start: 0.8034 (t0) cc_final: 0.7596 (t0) REVERT: E 62 GLN cc_start: 0.8909 (tp40) cc_final: 0.8652 (tp40) REVERT: E 71 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: M 156 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8990 (tp) REVERT: M 212 TRP cc_start: 0.7864 (m100) cc_final: 0.7408 (m100) REVERT: M 365 MET cc_start: 0.5399 (tpp) cc_final: 0.5194 (tpp) REVERT: M 460 LYS cc_start: 0.6760 (pttm) cc_final: 0.5936 (ptpt) outliers start: 96 outliers final: 54 residues processed: 292 average time/residue: 0.3731 time to fit residues: 180.9145 Evaluate side-chains 267 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 2.946 ------------------------------------------------------------------------------- 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 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 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 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 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 680 LEU 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 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 1220 GLN 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 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 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 1 optimal weight: 40.0000 chunk 210 optimal weight: 30.0000 chunk 220 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 253 optimal weight: 0.9980 chunk 368 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 686 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 = 0.3582 r_free = 0.3582 target = 0.085488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.054669 restraints weight = 97311.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056547 restraints weight = 45510.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057714 restraints weight = 28726.417| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 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 = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 29599 Z= 0.217 Angle : 0.606 10.686 40640 Z= 0.314 Chirality : 0.042 0.187 4823 Planarity : 0.005 0.122 4964 Dihedral : 16.227 176.704 5076 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 5.18 % Allowed : 25.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3609 helix: 1.37 (0.15), residues: 1304 sheet: 0.03 (0.26), residues: 383 loop : -1.43 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 183 HIS 0.004 0.001 HIS D 113 PHE 0.012 0.001 PHE M 397 TYR 0.018 0.001 TYR A 185 ARG 0.014 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 1213) hydrogen bonds : angle 4.08159 ( 3360) metal coordination : bond 0.00195 ( 3) covalent geometry : bond 0.00487 (29596) covalent geometry : angle 0.60607 (40640) *********************** 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 343 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 204 time to evaluate : 2.884 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 262 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8009 (tp) REVERT: A 283 GLN cc_start: 0.8993 (tt0) cc_final: 0.8755 (tt0) REVERT: B 194 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: C 201 ARG cc_start: 0.7012 (ttp80) cc_final: 0.6500 (mtp-110) REVERT: C 347 ILE cc_start: 0.6322 (mm) cc_final: 0.6032 (mm) REVERT: C 479 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8310 (tp) REVERT: C 538 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9065 (pp) REVERT: C 796 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8487 (pp) REVERT: C 936 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7882 (tpp80) REVERT: C 953 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9222 (tp) REVERT: C 954 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9297 (ptpp) REVERT: C 1009 ASN cc_start: 0.8894 (t0) cc_final: 0.8630 (m110) REVERT: C 1085 MET cc_start: 0.9541 (mmm) cc_final: 0.9058 (mmm) REVERT: C 1119 MET cc_start: 0.8661 (ttt) cc_final: 0.8441 (ttp) REVERT: C 1265 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8339 (t80) REVERT: C 1329 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7668 (mt-10) REVERT: D 37 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: D 248 ASP cc_start: 0.9047 (m-30) cc_final: 0.8658 (m-30) REVERT: D 264 ASP cc_start: 0.8705 (p0) cc_final: 0.8049 (p0) REVERT: D 267 ASP cc_start: 0.8693 (m-30) cc_final: 0.8264 (m-30) REVERT: D 298 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.7942 (mpp) REVERT: D 330 MET cc_start: 0.8473 (ppp) cc_final: 0.7809 (ppp) REVERT: D 332 LYS cc_start: 0.5403 (OUTLIER) cc_final: 0.5037 (mmtm) REVERT: D 484 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8486 (mtm) REVERT: D 558 ASP cc_start: 0.7016 (p0) cc_final: 0.6733 (p0) REVERT: D 960 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8069 (mt) REVERT: D 1366 HIS cc_start: 0.9396 (OUTLIER) cc_final: 0.9116 (m170) REVERT: E 15 ASN cc_start: 0.8507 (t0) cc_final: 0.7966 (t0) REVERT: E 62 GLN cc_start: 0.9006 (tp40) cc_final: 0.8773 (tp40) REVERT: E 67 ARG cc_start: 0.9175 (tpp80) cc_final: 0.8911 (tpp80) REVERT: E 71 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: M 156 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8967 (tp) REVERT: M 460 LYS cc_start: 0.6538 (pttm) cc_final: 0.5763 (ptpt) outliers start: 139 outliers final: 83 residues processed: 324 average time/residue: 0.3807 time to fit residues: 205.4825 Evaluate side-chains 297 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 197 time to evaluate : 2.994 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain A residue 262 LEU 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 B residue 217 ILE 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 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 414 ILE Chi-restraints excluded: chain C residue 479 LEU 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 680 LEU 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 954 LYS 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 117 LEU Chi-restraints excluded: chain D residue 124 ILE 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 332 LYS 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 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 891 ASP 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 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 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 271 TYR 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 19 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 280 optimal weight: 20.0000 chunk 300 optimal weight: 50.0000 chunk 210 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D1023 HIS M 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.053776 restraints weight = 97711.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.055630 restraints weight = 45511.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056799 restraints weight = 28774.857| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 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 = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29599 Z= 0.234 Angle : 0.615 11.395 40640 Z= 0.317 Chirality : 0.042 0.194 4823 Planarity : 0.004 0.089 4964 Dihedral : 16.288 176.544 5076 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 4.99 % Allowed : 25.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3609 helix: 1.39 (0.15), residues: 1304 sheet: -0.06 (0.26), residues: 385 loop : -1.44 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.003 0.001 HIS D1023 PHE 0.010 0.001 PHE M 397 TYR 0.022 0.001 TYR A 185 ARG 0.004 0.000 ARG D 259 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1213) hydrogen bonds : angle 4.08384 ( 3360) metal coordination : bond 0.00293 ( 3) covalent geometry : bond 0.00525 (29596) covalent geometry : angle 0.61520 (40640) *********************** 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 340 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 206 time to evaluate : 2.990 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 17 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8448 (pp20) REVERT: A 262 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 283 GLN cc_start: 0.9038 (tt0) cc_final: 0.8792 (tt0) REVERT: B 194 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: C 83 GLN cc_start: 0.9050 (mp10) cc_final: 0.8467 (pm20) REVERT: C 188 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: C 493 ILE cc_start: 0.7831 (pt) cc_final: 0.7236 (tt) REVERT: C 538 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9025 (pp) REVERT: C 653 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.7815 (tpt) REVERT: C 796 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.8748 (pp) REVERT: C 936 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8007 (tpp80) REVERT: C 953 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9296 (tp) REVERT: C 954 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9339 (ptpp) REVERT: C 959 ASP cc_start: 0.8844 (p0) cc_final: 0.8594 (p0) REVERT: C 1085 MET cc_start: 0.9547 (mmm) cc_final: 0.9135 (mmm) REVERT: C 1119 MET cc_start: 0.8676 (ttt) cc_final: 0.8464 (ttp) REVERT: C 1329 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7596 (mt-10) REVERT: D 37 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: D 248 ASP cc_start: 0.9014 (m-30) cc_final: 0.8657 (m-30) REVERT: D 264 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8049 (p0) REVERT: D 267 ASP cc_start: 0.8627 (m-30) cc_final: 0.8176 (m-30) REVERT: D 330 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7854 (ppp) REVERT: D 332 LYS cc_start: 0.5461 (OUTLIER) cc_final: 0.5013 (mmtm) REVERT: D 340 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7104 (mm-40) REVERT: D 484 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8435 (mtm) REVERT: D 869 CYS cc_start: 0.8891 (m) cc_final: 0.8639 (m) REVERT: D 960 LEU cc_start: 0.8325 (tp) cc_final: 0.8004 (mt) REVERT: D 1366 HIS cc_start: 0.9430 (OUTLIER) cc_final: 0.9155 (m170) REVERT: E 62 GLN cc_start: 0.9045 (tp40) cc_final: 0.8813 (tp40) REVERT: E 67 ARG cc_start: 0.9190 (tpp80) cc_final: 0.8963 (tpp80) REVERT: E 71 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: M 156 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8944 (tp) REVERT: M 202 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8881 (mt0) REVERT: M 460 LYS cc_start: 0.6522 (pttm) cc_final: 0.5739 (ptpt) outliers start: 134 outliers final: 82 residues processed: 319 average time/residue: 0.3899 time to fit residues: 206.8511 Evaluate side-chains 298 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 197 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU 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 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 188 PHE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 553 THR 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 764 CYS 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 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 111 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 264 ASP Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 332 LYS 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 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 958 ILE 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 1198 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 202 GLN Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 271 TYR 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 19 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 366 optimal weight: 20.0000 chunk 238 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 ASN M 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054570 restraints weight = 97203.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.056465 restraints weight = 45026.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057601 restraints weight = 28302.329| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 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 = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29599 Z= 0.152 Angle : 0.582 10.569 40640 Z= 0.297 Chirality : 0.041 0.285 4823 Planarity : 0.004 0.082 4964 Dihedral : 16.273 176.392 5076 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 4.21 % Allowed : 26.38 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3609 helix: 1.46 (0.15), residues: 1304 sheet: -0.04 (0.26), residues: 385 loop : -1.40 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 115 HIS 0.003 0.001 HIS C1070 PHE 0.010 0.001 PHE C1323 TYR 0.018 0.001 TYR A 185 ARG 0.012 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 1213) hydrogen bonds : angle 3.97788 ( 3360) metal coordination : bond 0.00194 ( 3) covalent geometry : bond 0.00341 (29596) covalent geometry : angle 0.58235 (40640) *********************** 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 320 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 207 time to evaluate : 2.848 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: 0.8610 (OUTLIER) cc_final: 0.8278 (tp) REVERT: B 76 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: C 81 ASP cc_start: 0.8239 (p0) cc_final: 0.7850 (p0) REVERT: C 83 GLN cc_start: 0.9043 (mp10) cc_final: 0.8588 (pm20) REVERT: C 188 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7729 (m-10) REVERT: C 493 ILE cc_start: 0.7749 (pt) cc_final: 0.7203 (tt) REVERT: C 538 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9020 (pp) REVERT: C 542 ARG cc_start: 0.8176 (mmp80) cc_final: 0.7543 (mtt90) REVERT: C 618 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7825 (tp40) REVERT: C 653 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.7808 (tpt) REVERT: C 796 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8658 (pp) REVERT: C 936 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7938 (tpp80) REVERT: C 953 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9296 (tp) REVERT: C 954 LYS cc_start: 0.9568 (OUTLIER) cc_final: 0.9326 (ptpp) REVERT: C 1009 ASN cc_start: 0.9038 (t0) cc_final: 0.8610 (m110) REVERT: C 1041 ASP cc_start: 0.8532 (t0) cc_final: 0.8149 (p0) REVERT: C 1085 MET cc_start: 0.9528 (mmm) cc_final: 0.9107 (mmm) REVERT: C 1119 MET cc_start: 0.8638 (ttt) cc_final: 0.8435 (ttp) REVERT: C 1329 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7596 (mt-10) REVERT: D 37 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: D 115 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.7663 (m-90) REVERT: D 248 ASP cc_start: 0.8979 (m-30) cc_final: 0.8630 (m-30) REVERT: D 264 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8048 (p0) REVERT: D 267 ASP cc_start: 0.8639 (m-30) cc_final: 0.8170 (m-30) REVERT: D 330 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7972 (ppp) REVERT: D 332 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.5003 (mmtm) REVERT: D 340 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7036 (mm-40) REVERT: D 504 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: D 960 LEU cc_start: 0.8298 (tp) cc_final: 0.7958 (mt) REVERT: D 1366 HIS cc_start: 0.9388 (OUTLIER) cc_final: 0.9131 (m170) REVERT: E 15 ASN cc_start: 0.8379 (t0) cc_final: 0.7986 (t0) REVERT: E 62 GLN cc_start: 0.9033 (tp40) cc_final: 0.8801 (tp40) REVERT: E 71 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: M 156 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8966 (tp) REVERT: M 460 LYS cc_start: 0.6541 (pttm) cc_final: 0.5774 (ptpt) outliers start: 113 outliers final: 75 residues processed: 299 average time/residue: 0.3728 time to fit residues: 184.8042 Evaluate side-chains 293 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 199 time to evaluate : 2.849 ------------------------------------------------------------------------------- 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 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 276 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 76 GLU 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 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 199 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 289 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 400 VAL 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 618 GLN 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 745 GLU 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 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 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 111 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 GLN 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 839 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 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 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 201 ILE Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 271 TYR 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 313 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 337 optimal weight: 5.9990 chunk 163 optimal weight: 40.0000 chunk 279 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3563 r_free = 0.3563 target = 0.084385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.053759 restraints weight = 97829.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055627 restraints weight = 45512.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.056800 restraints weight = 28691.622| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29599 Z= 0.199 Angle : 0.606 12.554 40640 Z= 0.309 Chirality : 0.042 0.356 4823 Planarity : 0.004 0.077 4964 Dihedral : 16.281 176.286 5076 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 4.43 % Allowed : 26.19 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3609 helix: 1.47 (0.15), residues: 1302 sheet: -0.01 (0.27), residues: 379 loop : -1.40 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.003 0.001 HIS D1023 PHE 0.012 0.001 PHE C 545 TYR 0.018 0.001 TYR A 185 ARG 0.006 0.000 ARG C 436 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 1213) hydrogen bonds : angle 4.01000 ( 3360) metal coordination : bond 0.00204 ( 3) covalent geometry : bond 0.00446 (29596) covalent geometry : angle 0.60576 (40640) *********************** 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: 119 poor density : 206 time to evaluate : 2.974 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 283 GLN cc_start: 0.9199 (tt0) cc_final: 0.8964 (tp40) REVERT: B 76 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: C 14 ASP cc_start: 0.8454 (t0) cc_final: 0.8155 (t0) REVERT: C 83 GLN cc_start: 0.9057 (mp10) cc_final: 0.8672 (pm20) REVERT: C 188 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: C 238 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7551 (mp10) REVERT: C 493 ILE cc_start: 0.7788 (pt) cc_final: 0.7305 (tt) REVERT: C 538 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9036 (pp) REVERT: C 542 ARG cc_start: 0.8180 (mmp80) cc_final: 0.7496 (ttt90) REVERT: C 618 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7810 (mm-40) REVERT: C 653 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.7817 (tpt) REVERT: C 796 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.8653 (pp) REVERT: C 936 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7982 (tpp80) REVERT: C 953 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9341 (tp) REVERT: C 954 LYS cc_start: 0.9568 (OUTLIER) cc_final: 0.9332 (ptpp) REVERT: C 1009 ASN cc_start: 0.9094 (t0) cc_final: 0.8702 (m-40) REVERT: C 1041 ASP cc_start: 0.8509 (t0) cc_final: 0.8121 (p0) REVERT: C 1085 MET cc_start: 0.9544 (mmm) cc_final: 0.9162 (mmm) REVERT: C 1329 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7609 (mt-10) REVERT: D 37 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7311 (tp30) REVERT: D 115 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.7741 (m-90) REVERT: D 248 ASP cc_start: 0.8984 (m-30) cc_final: 0.8654 (m-30) REVERT: D 264 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8050 (p0) REVERT: D 267 ASP cc_start: 0.8639 (m-30) cc_final: 0.8209 (m-30) REVERT: D 330 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7934 (ppp) REVERT: D 332 LYS cc_start: 0.5508 (OUTLIER) cc_final: 0.5059 (mmtm) REVERT: D 340 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7117 (mm-40) REVERT: D 478 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9310 (mm) REVERT: D 484 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8360 (mtm) REVERT: D 504 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: D 869 CYS cc_start: 0.8833 (m) cc_final: 0.8613 (m) REVERT: D 960 LEU cc_start: 0.8362 (tp) cc_final: 0.8016 (mt) REVERT: D 1366 HIS cc_start: 0.9407 (OUTLIER) cc_final: 0.9155 (m170) REVERT: E 15 ASN cc_start: 0.8437 (t0) cc_final: 0.7875 (t0) REVERT: E 62 GLN cc_start: 0.9044 (tp40) cc_final: 0.8830 (tp40) REVERT: E 71 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: M 156 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8926 (tp) REVERT: M 460 LYS cc_start: 0.6530 (pttm) cc_final: 0.5771 (ptpt) outliers start: 119 outliers final: 82 residues processed: 306 average time/residue: 0.3863 time to fit residues: 196.2871 Evaluate side-chains 300 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 198 time to evaluate : 3.361 ------------------------------------------------------------------------------- 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 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 76 GLU 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 198 ILE Chi-restraints excluded: chain C residue 199 ASP 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 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 653 MET Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 745 GLU 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 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 111 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 332 LYS 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 504 GLN 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 891 ASP Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 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 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 201 ILE Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 271 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 293 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 316 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 135 optimal weight: 0.0770 chunk 290 optimal weight: 50.0000 chunk 355 optimal weight: 40.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.085090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.054552 restraints weight = 96840.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056451 restraints weight = 44765.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057637 restraints weight = 28063.761| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 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 = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2992 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= 0.140 Angle : 0.583 13.977 40640 Z= 0.296 Chirality : 0.041 0.290 4823 Planarity : 0.004 0.077 4964 Dihedral : 16.276 176.825 5076 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 3.87 % Allowed : 26.71 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3609 helix: 1.52 (0.15), residues: 1304 sheet: 0.11 (0.26), residues: 384 loop : -1.39 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.003 0.001 HIS D 430 PHE 0.011 0.001 PHE C 545 TYR 0.022 0.001 TYR A 185 ARG 0.018 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 1213) hydrogen bonds : angle 3.92142 ( 3360) metal coordination : bond 0.00161 ( 3) covalent geometry : bond 0.00316 (29596) covalent geometry : angle 0.58324 (40640) *********************** 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 311 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 207 time to evaluate : 3.200 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: 0.8682 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 283 GLN cc_start: 0.9154 (tt0) cc_final: 0.8910 (tp40) REVERT: B 76 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: B 194 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: C 14 ASP cc_start: 0.8458 (t0) cc_final: 0.8193 (t0) REVERT: C 83 GLN cc_start: 0.9077 (mp10) cc_final: 0.8719 (pm20) REVERT: C 188 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: C 493 ILE cc_start: 0.7789 (pt) cc_final: 0.7328 (tt) REVERT: C 538 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9041 (pp) REVERT: C 542 ARG cc_start: 0.8161 (mmp80) cc_final: 0.7515 (ttt90) REVERT: C 549 ASP cc_start: 0.8766 (m-30) cc_final: 0.8486 (m-30) REVERT: C 796 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.8634 (pp) REVERT: C 930 ASP cc_start: 0.8004 (t0) cc_final: 0.7796 (t0) REVERT: C 953 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9344 (tp) REVERT: C 954 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9339 (ptmm) REVERT: C 1009 ASN cc_start: 0.9117 (t0) cc_final: 0.8732 (m-40) REVERT: C 1041 ASP cc_start: 0.8509 (t0) cc_final: 0.8118 (p0) REVERT: C 1085 MET cc_start: 0.9523 (mmm) cc_final: 0.9076 (mmm) REVERT: C 1329 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 37 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: D 248 ASP cc_start: 0.8975 (m-30) cc_final: 0.8631 (m-30) REVERT: D 264 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8023 (p0) REVERT: D 267 ASP cc_start: 0.8652 (m-30) cc_final: 0.8199 (m-30) REVERT: D 330 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7953 (ppp) REVERT: D 332 LYS cc_start: 0.5434 (OUTLIER) cc_final: 0.4816 (mmtm) REVERT: D 340 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7067 (mm-40) REVERT: D 504 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: D 869 CYS cc_start: 0.8792 (m) cc_final: 0.8573 (m) REVERT: D 960 LEU cc_start: 0.8305 (tp) cc_final: 0.7945 (mt) REVERT: D 1366 HIS cc_start: 0.9382 (OUTLIER) cc_final: 0.9073 (m170) REVERT: E 62 GLN cc_start: 0.9017 (tp40) cc_final: 0.8802 (tp40) REVERT: E 71 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: M 156 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8960 (tp) REVERT: M 460 LYS cc_start: 0.6519 (pttm) cc_final: 0.5757 (ptpt) outliers start: 104 outliers final: 78 residues processed: 295 average time/residue: 0.3952 time to fit residues: 193.6350 Evaluate side-chains 295 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 201 time to evaluate : 3.164 ------------------------------------------------------------------------------- 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 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 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 GLU 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 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 289 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 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 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 745 GLU 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 838 CYS Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 954 LYS 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 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 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 124 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 GLN 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 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 1198 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 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 201 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 310 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 318 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055641 restraints weight = 96702.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057563 restraints weight = 44513.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058764 restraints weight = 27804.823| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 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 = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29599 Z= 0.116 Angle : 0.583 17.971 40640 Z= 0.292 Chirality : 0.041 0.287 4823 Planarity : 0.004 0.074 4964 Dihedral : 16.250 177.680 5076 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer: Outliers : 3.39 % Allowed : 27.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3609 helix: 1.59 (0.15), residues: 1302 sheet: 0.22 (0.27), residues: 381 loop : -1.35 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 212 HIS 0.003 0.001 HIS D 430 PHE 0.012 0.001 PHE C 545 TYR 0.020 0.001 TYR A 185 ARG 0.006 0.000 ARG C 436 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 1213) hydrogen bonds : angle 3.86597 ( 3360) metal coordination : bond 0.00103 ( 3) covalent geometry : bond 0.00261 (29596) covalent geometry : angle 0.58276 (40640) ********************** 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 301 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 210 time to evaluate : 3.792 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: 0.8222 (mmm) cc_final: 0.7999 (tpp) REVERT: A 262 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8344 (tp) REVERT: A 283 GLN cc_start: 0.9152 (tt0) cc_final: 0.8882 (tp40) REVERT: B 76 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: B 194 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: C 14 ASP cc_start: 0.8385 (t0) cc_final: 0.8101 (t0) REVERT: C 83 GLN cc_start: 0.9107 (mp10) cc_final: 0.8746 (pm20) REVERT: C 188 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: C 493 ILE cc_start: 0.7880 (pt) cc_final: 0.7401 (tt) REVERT: C 538 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9038 (pp) REVERT: C 542 ARG cc_start: 0.8196 (mmp80) cc_final: 0.7625 (ttt90) REVERT: C 549 ASP cc_start: 0.8725 (m-30) cc_final: 0.8237 (m-30) REVERT: C 653 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.7942 (tpt) REVERT: C 796 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8601 (pp) REVERT: C 930 ASP cc_start: 0.7968 (t0) cc_final: 0.7758 (t0) REVERT: C 953 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9333 (tp) REVERT: C 954 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9332 (ptmm) REVERT: C 1009 ASN cc_start: 0.9087 (t0) cc_final: 0.8719 (m-40) REVERT: C 1018 TYR cc_start: 0.8968 (t80) cc_final: 0.8589 (t80) REVERT: C 1329 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 248 ASP cc_start: 0.8950 (m-30) cc_final: 0.8629 (m-30) REVERT: D 264 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8002 (p0) REVERT: D 267 ASP cc_start: 0.8675 (m-30) cc_final: 0.8186 (m-30) REVERT: D 330 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7888 (ppp) REVERT: D 332 LYS cc_start: 0.5575 (OUTLIER) cc_final: 0.4949 (mmtm) REVERT: D 484 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8589 (mmm) REVERT: D 504 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: D 960 LEU cc_start: 0.8298 (tp) cc_final: 0.7924 (mt) REVERT: D 1366 HIS cc_start: 0.9358 (OUTLIER) cc_final: 0.9009 (m170) REVERT: E 15 ASN cc_start: 0.8181 (t0) cc_final: 0.7864 (t0) REVERT: E 62 GLN cc_start: 0.9001 (tp40) cc_final: 0.8796 (tp40) REVERT: E 71 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8566 (mp0) REVERT: M 156 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8966 (tp) REVERT: M 460 LYS cc_start: 0.6423 (pttm) cc_final: 0.5709 (ptpt) outliers start: 91 outliers final: 70 residues processed: 284 average time/residue: 0.3838 time to fit residues: 184.0662 Evaluate side-chains 287 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 200 time to evaluate : 3.109 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 129 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 103 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 289 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 400 VAL Chi-restraints excluded: chain C residue 403 MET 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 745 GLU 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 854 ILE Chi-restraints excluded: chain C residue 884 VAL 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 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 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 124 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 332 LYS 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 504 GLN 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 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 1163 VAL Chi-restraints excluded: chain D residue 1198 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 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 201 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 344 optimal weight: 9.9990 chunk 298 optimal weight: 50.0000 chunk 244 optimal weight: 7.9990 chunk 273 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 310 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 ASN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.054716 restraints weight = 96780.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056608 restraints weight = 44720.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057784 restraints weight = 28034.223| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 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 = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29599 Z= 0.155 Angle : 0.595 16.446 40640 Z= 0.299 Chirality : 0.041 0.309 4823 Planarity : 0.004 0.076 4964 Dihedral : 16.270 177.999 5076 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 3.95 % Allowed : 26.68 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3609 helix: 1.60 (0.15), residues: 1303 sheet: 0.14 (0.26), residues: 390 loop : -1.34 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.003 0.001 HIS C1070 PHE 0.012 0.001 PHE C 545 TYR 0.021 0.001 TYR A 185 ARG 0.019 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 1213) hydrogen bonds : angle 3.87519 ( 3360) metal coordination : bond 0.00183 ( 3) covalent geometry : bond 0.00352 (29596) covalent geometry : angle 0.59479 (40640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10896.86 seconds wall clock time: 190 minutes 34.11 seconds (11434.11 seconds total)