Starting phenix.real_space_refine on Wed Jun 25 13:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8igr_35438/06_2025/8igr_35438.cif Found real_map, /net/cci-nas-00/data/ceres_data/8igr_35438/06_2025/8igr_35438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8igr_35438/06_2025/8igr_35438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8igr_35438/06_2025/8igr_35438.map" model { file = "/net/cci-nas-00/data/ceres_data/8igr_35438/06_2025/8igr_35438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8igr_35438/06_2025/8igr_35438.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 122 5.49 5 Mg 1 5.21 5 S 127 5.16 5 C 18481 2.51 5 N 5336 2.21 5 O 5974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30043 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2254 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 9176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9176 Classifications: {'peptide': 1167} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1114} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 9022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 9022 Classifications: {'peptide': 1154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1106} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "L" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2500 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 577 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 587 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} bond proxies already assigned to first conformer: 588 Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "N" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1247 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "T" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1254 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "J" 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 13557 SG CYS J 70 62.328 117.543 61.629 1.00 64.95 S ATOM 13571 SG CYS J 72 63.204 121.129 62.066 1.00 59.35 S ATOM 13679 SG CYS J 85 60.786 120.084 59.277 1.00 60.83 S ATOM 13703 SG CYS J 88 64.424 118.649 59.164 1.00 54.04 S ATOM 19385 SG CYS J 814 61.934 51.403 52.012 1.00 24.88 S ATOM 19950 SG CYS J 888 64.250 54.281 52.863 1.00 15.26 S ATOM 20001 SG CYS J 895 62.069 52.638 55.617 1.00 17.04 S ATOM 20022 SG CYS J 898 65.034 50.894 54.292 1.00 17.85 S Time building chain proxies: 17.16, per 1000 atoms: 0.57 Number of scatterers: 30043 At special positions: 0 Unit cell: (151.13, 168.98, 149.94, 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 127 16.00 P 122 15.00 Mg 1 11.99 O 5974 8.00 N 5336 7.00 C 18481 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: 8.60 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J2002 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 70 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 85 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 72 " pdb="ZN ZN J2002 " - pdb=" SG CYS J 88 " pdb=" ZN J2003 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 895 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 898 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 888 " pdb="ZN ZN J2003 " - pdb=" SG CYS J 814 " Number of angles added : 12 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6526 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 42 sheets defined 48.4% alpha, 13.2% beta 47 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 12.27 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.512A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 3.989A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 260 Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 277 through 282 Processing helix chain 'G' and resid 285 through 291 removed outlier: 3.755A pdb=" N LYS G 291 " --> pdb=" O VAL G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 310 Processing helix chain 'H' and resid 34 through 50 Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.514A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.650A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.649A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 347 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.981A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 removed outlier: 4.462A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.637A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.617A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.506A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.838A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.529A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 942 through 967 Processing helix chain 'I' and resid 1022 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.377A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.604A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.684A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1293 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.816A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.595A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.795A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.833A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.723A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.956A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.820A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 515 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.858A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.581A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 636 removed outlier: 3.712A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.938A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 788 removed outlier: 3.714A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 805 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1138 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.223A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.565A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.724A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 Processing helix chain 'J' and resid 1361 through 1374 removed outlier: 4.602A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 14 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 76 removed outlier: 3.678A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 114 through 136 removed outlier: 3.659A pdb=" N ASP L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 366 through 374 Processing helix chain 'L' and resid 376 through 383 Processing helix chain 'L' and resid 383 through 390 removed outlier: 3.549A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE L 388 " --> pdb=" O LEU L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 395 removed outlier: 3.874A pdb=" N THR L 395 " --> pdb=" O LYS L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.706A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.749A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.597A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 482 through 487 removed outlier: 3.542A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 500 removed outlier: 3.972A pdb=" N ARG L 495 " --> pdb=" O GLU L 491 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.851A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 549 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 604 through 610 Processing helix chain 'A' and resid 8 through 25 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.846A pdb=" N ARG A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.941A pdb=" N TRP A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 25 through 33 Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 39 through 58 removed outlier: 3.759A pdb=" N ILE B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.914A pdb=" N ALA B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.732A pdb=" N ARG C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 64 through 79 Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 39 through 59 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 61 through 78 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.975A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.371A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.488A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 4.053A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 53 through 61 removed outlier: 6.617A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.666A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.071A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 157 Processing sheet with id=AB8, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.485A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.328A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.773A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.297A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AC7, first strand: chain 'I' and resid 830 through 831 Processing sheet with id=AC8, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.093A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.601A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.578A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.432A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD6, first strand: chain 'J' and resid 252 through 255 removed outlier: 6.512A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 350 through 356 removed outlier: 6.176A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 707 removed outlier: 3.787A pdb=" N ILE J 707 " --> pdb=" O GLU J 714 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 removed outlier: 6.111A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU J 811 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.903A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 3.591A pdb=" N VAL J 848 " --> pdb=" O VAL J 858 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1187 through 1189 Processing sheet with id=AE6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.725A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 16.63 Time building geometry restraints manager: 10.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5010 1.32 - 1.44: 7889 1.44 - 1.57: 17372 1.57 - 1.69: 242 1.69 - 1.81: 225 Bond restraints: 30738 Sorted by residual: bond pdb=" N ILE I 59 " pdb=" CA ILE I 59 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL I 196 " pdb=" CA VAL I 196 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.02e+01 bond pdb=" N PHE I 57 " pdb=" CA PHE I 57 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 1.02e+01 bond pdb=" C PRO J 51 " pdb=" O PRO J 51 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL I 56 " pdb=" CA VAL I 56 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.78e+00 ... (remaining 30733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 40653 1.50 - 3.01: 1153 3.01 - 4.51: 190 4.51 - 6.02: 23 6.02 - 7.52: 6 Bond angle restraints: 42025 Sorted by residual: angle pdb=" N ARG J 53 " pdb=" CA ARG J 53 " pdb=" C ARG J 53 " ideal model delta sigma weight residual 111.07 116.02 -4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" N VAL H 192 " pdb=" CA VAL H 192 " pdb=" C VAL H 192 " ideal model delta sigma weight residual 110.21 105.22 4.99 1.13e+00 7.83e-01 1.95e+01 angle pdb=" CA ARG J 53 " pdb=" C ARG J 53 " pdb=" O ARG J 53 " ideal model delta sigma weight residual 120.82 116.20 4.62 1.05e+00 9.07e-01 1.94e+01 angle pdb=" C THR I 91 " pdb=" CA THR I 91 " pdb=" CB THR I 91 " ideal model delta sigma weight residual 110.22 103.45 6.77 1.67e+00 3.59e-01 1.64e+01 angle pdb=" N GLN I 490 " pdb=" CA GLN I 490 " pdb=" C GLN I 490 " ideal model delta sigma weight residual 114.56 109.56 5.00 1.27e+00 6.20e-01 1.55e+01 ... (remaining 42020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 17368 34.98 - 69.95: 1202 69.95 - 104.93: 66 104.93 - 139.91: 2 139.91 - 174.88: 1 Dihedral angle restraints: 18639 sinusoidal: 8531 harmonic: 10108 Sorted by residual: dihedral pdb=" C ASP I 199 " pdb=" N ASP I 199 " pdb=" CA ASP I 199 " pdb=" CB ASP I 199 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" N ASP I 199 " pdb=" C ASP I 199 " pdb=" CA ASP I 199 " pdb=" CB ASP I 199 " ideal model delta harmonic sigma weight residual 122.80 136.23 -13.43 0 2.50e+00 1.60e-01 2.89e+01 dihedral pdb=" CA TRP I 807 " pdb=" C TRP I 807 " pdb=" N ASN I 808 " pdb=" CA ASN I 808 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 18636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4612 0.100 - 0.200: 190 0.200 - 0.301: 2 0.301 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA ASP I 199 " pdb=" N ASP I 199 " pdb=" C ASP I 199 " pdb=" CB ASP I 199 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA PHE I 57 " pdb=" N PHE I 57 " pdb=" C PHE I 57 " pdb=" CB PHE I 57 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR I 91 " pdb=" N THR I 91 " pdb=" C THR I 91 " pdb=" CB THR I 91 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4803 not shown) Planarity restraints: 5039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 196 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C VAL I 196 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL I 196 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG I 197 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER J 492 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO J 493 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 493 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 493 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN J 45 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASN J 45 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN J 45 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR J 46 " -0.010 2.00e-02 2.50e+03 ... (remaining 5036 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 71 2.41 - 3.03: 18232 3.03 - 3.65: 45282 3.65 - 4.28: 71263 4.28 - 4.90: 116679 Nonbonded interactions: 251527 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J2001 " model vdw 1.787 2.170 nonbonded pdb=" NZ LYS I 890 " pdb=" O SER I 911 " model vdw 2.212 3.120 nonbonded pdb=" O TYR I 346 " pdb=" OG1 THR I 350 " model vdw 2.218 3.040 nonbonded pdb=" O VAL L 130 " pdb=" OG SER L 133 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP A 36 " pdb=" N LYS A 37 " model vdw 2.225 3.120 ... (remaining 251522 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 71 or resid 73 through 78)) selection = (chain 'B' and (resid 8 through 71 or resid 73 through 78)) selection = (chain 'C' and (resid 8 through 71 or resid 73 through 78)) selection = (chain 'D' and (resid 8 through 71 or resid 73 through 78)) } 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=0.13 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.030 Extract box with map and model: 1.370 Check model and map are aligned: 0.250 Set scattering table: 0.270 Process input model: 93.720 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.053 30746 Z= 0.211 Angle : 0.623 14.585 42037 Z= 0.352 Chirality : 0.044 0.501 4806 Planarity : 0.005 0.046 5039 Dihedral : 20.464 174.883 12113 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.60 % Allowed : 19.80 % Favored : 79.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3478 helix: 0.75 (0.13), residues: 1545 sheet: -0.97 (0.24), residues: 385 loop : -1.22 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 43 HIS 0.007 0.001 HIS I1023 PHE 0.025 0.002 PHE J 227 TYR 0.017 0.002 TYR G 177 ARG 0.006 0.000 ARG I 779 Details of bonding type rmsd hydrogen bonds : bond 0.14095 ( 1421) hydrogen bonds : angle 6.24766 ( 3977) metal coordination : bond 0.00642 ( 8) metal coordination : angle 5.65055 ( 12) covalent geometry : bond 0.00456 (30738) covalent geometry : angle 0.61580 (42025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 419 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.7908 (tp) cc_final: 0.7490 (tp) outliers start: 18 outliers final: 4 residues processed: 431 average time/residue: 0.4906 time to fit residues: 319.0350 Evaluate side-chains 305 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 301 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 799 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 325 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS G 268 ASN H 186 ASN I 165 HIS I 811 ASN I1209 GLN J1218 HIS L 406 GLN L 455 HIS A 8 ASN C 8 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.056489 restraints weight = 68403.639| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.57 r_work: 0.2675 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30746 Z= 0.218 Angle : 0.638 8.551 42037 Z= 0.338 Chirality : 0.043 0.182 4806 Planarity : 0.004 0.049 5039 Dihedral : 18.302 179.805 5224 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.09 % Allowed : 20.37 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3478 helix: 1.21 (0.13), residues: 1581 sheet: -0.66 (0.25), residues: 377 loop : -1.10 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 43 HIS 0.014 0.001 HIS I 165 PHE 0.030 0.002 PHE B 51 TYR 0.019 0.001 TYR G 177 ARG 0.006 0.001 ARG J 259 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 1421) hydrogen bonds : angle 4.75328 ( 3977) metal coordination : bond 0.00948 ( 8) metal coordination : angle 3.98273 ( 12) covalent geometry : bond 0.00507 (30738) covalent geometry : angle 0.63466 (42025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 312 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 105 TYR cc_start: 0.8154 (m-10) cc_final: 0.7937 (m-10) REVERT: I 582 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8198 (m110) REVERT: I 592 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8306 (ptm160) REVERT: I 596 ASP cc_start: 0.8383 (p0) cc_final: 0.8066 (p0) REVERT: I 740 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8945 (mt-10) REVERT: I 1025 PHE cc_start: 0.7266 (t80) cc_final: 0.7049 (t80) REVERT: I 1170 MET cc_start: 0.9221 (mmp) cc_final: 0.9006 (mmm) REVERT: I 1304 MET cc_start: 0.9385 (tpt) cc_final: 0.9142 (tpp) REVERT: J 53 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7713 (tpt170) REVERT: J 330 MET cc_start: 0.8923 (mtp) cc_final: 0.8640 (mtp) REVERT: J 764 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8736 (ttt-90) REVERT: K 62 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 27 GLU cc_start: 0.8216 (tp30) cc_final: 0.7975 (tp30) REVERT: A 72 ARG cc_start: 0.9135 (ptp-110) cc_final: 0.8762 (ptt-90) REVERT: B 12 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8589 (ptm-80) REVERT: B 14 GLU cc_start: 0.9060 (tt0) cc_final: 0.8727 (tt0) REVERT: B 20 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9085 (mtmm) REVERT: B 33 VAL cc_start: 0.9275 (m) cc_final: 0.9003 (p) REVERT: B 51 PHE cc_start: 0.8604 (t80) cc_final: 0.8390 (t80) REVERT: B 53 MET cc_start: 0.8729 (tpp) cc_final: 0.8375 (tpp) REVERT: B 66 ASP cc_start: 0.7680 (m-30) cc_final: 0.7343 (t0) REVERT: B 69 ARG cc_start: 0.8462 (ttp80) cc_final: 0.7918 (ttp-170) REVERT: C 23 MET cc_start: 0.8770 (mmm) cc_final: 0.8419 (mmm) REVERT: C 73 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8302 (mm-40) outliers start: 92 outliers final: 45 residues processed: 382 average time/residue: 0.4246 time to fit residues: 257.5585 Evaluate side-chains 343 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 6.9990 chunk 330 optimal weight: 0.0020 chunk 256 optimal weight: 0.7980 chunk 284 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 213 optimal weight: 0.0870 chunk 258 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 overall best weight: 1.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 200 GLN J 364 HIS J 365 GLN C 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.057833 restraints weight = 68409.625| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.57 r_work: 0.2712 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30746 Z= 0.137 Angle : 0.563 9.439 42037 Z= 0.299 Chirality : 0.040 0.164 4806 Planarity : 0.004 0.049 5039 Dihedral : 18.047 179.687 5222 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.29 % Allowed : 20.84 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3478 helix: 1.49 (0.13), residues: 1567 sheet: -0.60 (0.26), residues: 356 loop : -0.92 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.010 0.001 HIS I 165 PHE 0.016 0.001 PHE J1325 TYR 0.017 0.001 TYR G 177 ARG 0.004 0.000 ARG I1171 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1421) hydrogen bonds : angle 4.43310 ( 3977) metal coordination : bond 0.00657 ( 8) metal coordination : angle 2.91125 ( 12) covalent geometry : bond 0.00312 (30738) covalent geometry : angle 0.56048 (42025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 315 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: H 218 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8126 (mtm-85) REVERT: I 105 TYR cc_start: 0.8293 (m-10) cc_final: 0.7901 (m-10) REVERT: I 370 MET cc_start: 0.8831 (mmm) cc_final: 0.8451 (mmm) REVERT: I 562 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: I 596 ASP cc_start: 0.8375 (p0) cc_final: 0.8010 (p0) REVERT: I 1028 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8751 (mmtm) REVERT: I 1170 MET cc_start: 0.9176 (mmp) cc_final: 0.8954 (mmm) REVERT: I 1304 MET cc_start: 0.9340 (tpt) cc_final: 0.9041 (tpp) REVERT: I 1310 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8313 (p0) REVERT: J 53 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7690 (tpt170) REVERT: J 160 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7940 (mt) REVERT: J 227 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.7736 (t80) REVERT: J 330 MET cc_start: 0.8925 (mtp) cc_final: 0.8581 (mtp) REVERT: J 386 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: J 764 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8803 (ttt-90) REVERT: J 1165 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: K 62 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7970 (tm-30) REVERT: L 137 TYR cc_start: 0.6637 (t80) cc_final: 0.6236 (t80) REVERT: L 546 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8578 (p0) REVERT: A 20 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8794 (mmmm) REVERT: A 27 GLU cc_start: 0.8116 (tp30) cc_final: 0.7822 (tp30) REVERT: A 69 ARG cc_start: 0.9161 (mtp-110) cc_final: 0.8723 (mtp180) REVERT: A 72 ARG cc_start: 0.9090 (ptp-110) cc_final: 0.8659 (ptt-90) REVERT: B 12 ARG cc_start: 0.8862 (ttt180) cc_final: 0.8605 (ttp80) REVERT: B 14 GLU cc_start: 0.9055 (tt0) cc_final: 0.8639 (tt0) REVERT: B 20 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9116 (mtmm) REVERT: B 24 LEU cc_start: 0.9394 (tp) cc_final: 0.9152 (tt) REVERT: B 28 LYS cc_start: 0.9241 (mtpt) cc_final: 0.8806 (mmmm) REVERT: B 31 GLU cc_start: 0.8912 (pt0) cc_final: 0.8321 (pt0) REVERT: B 46 ASP cc_start: 0.8914 (m-30) cc_final: 0.8659 (m-30) REVERT: B 51 PHE cc_start: 0.8624 (t80) cc_final: 0.8371 (t80) REVERT: B 53 MET cc_start: 0.8821 (tpp) cc_final: 0.8404 (tpp) REVERT: B 66 ASP cc_start: 0.7688 (m-30) cc_final: 0.7400 (t0) REVERT: B 69 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8195 (ttp-170) REVERT: C 6 LYS cc_start: 0.7036 (mmmm) cc_final: 0.6679 (mmmm) REVERT: C 73 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8336 (mm-40) REVERT: D 27 GLU cc_start: 0.8815 (pm20) cc_final: 0.8123 (tm-30) REVERT: D 28 LYS cc_start: 0.9526 (mmpt) cc_final: 0.9080 (mtpt) REVERT: D 31 GLU cc_start: 0.9273 (pt0) cc_final: 0.8800 (pt0) REVERT: D 51 PHE cc_start: 0.8848 (m-10) cc_final: 0.8630 (m-80) outliers start: 98 outliers final: 47 residues processed: 390 average time/residue: 0.4643 time to fit residues: 286.5228 Evaluate side-chains 358 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1310 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 209 optimal weight: 4.9990 chunk 325 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 306 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 357 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 811 ASN J 365 GLN J 651 HIS J 739 GLN L 383 ASN C 8 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.055281 restraints weight = 68678.009| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.55 r_work: 0.2652 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30746 Z= 0.245 Angle : 0.616 8.166 42037 Z= 0.325 Chirality : 0.042 0.161 4806 Planarity : 0.004 0.049 5039 Dihedral : 18.081 179.646 5221 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.86 % Allowed : 21.14 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3478 helix: 1.47 (0.13), residues: 1566 sheet: -0.63 (0.25), residues: 380 loop : -0.92 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.005 0.001 HIS G 23 PHE 0.021 0.002 PHE J1325 TYR 0.015 0.001 TYR G 177 ARG 0.008 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 1421) hydrogen bonds : angle 4.43718 ( 3977) metal coordination : bond 0.01021 ( 8) metal coordination : angle 3.38270 ( 12) covalent geometry : bond 0.00577 (30738) covalent geometry : angle 0.61307 (42025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 309 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: G 297 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9076 (mtpp) REVERT: H 192 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8169 (m) REVERT: H 218 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8101 (mtm-85) REVERT: I 69 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: I 105 TYR cc_start: 0.8409 (m-10) cc_final: 0.8206 (m-10) REVERT: I 165 HIS cc_start: 0.8753 (t-170) cc_final: 0.8501 (t-90) REVERT: I 370 MET cc_start: 0.8972 (mmm) cc_final: 0.8614 (mmm) REVERT: I 592 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8347 (ptm160) REVERT: I 637 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7767 (ptt-90) REVERT: I 1025 PHE cc_start: 0.7119 (t80) cc_final: 0.6449 (t80) REVERT: I 1028 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8756 (mmtm) REVERT: I 1170 MET cc_start: 0.9216 (mmp) cc_final: 0.8994 (mmm) REVERT: I 1304 MET cc_start: 0.9384 (tpt) cc_final: 0.9117 (tpp) REVERT: J 53 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7739 (tpt170) REVERT: J 160 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7961 (mt) REVERT: J 227 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8089 (t80) REVERT: J 330 MET cc_start: 0.8966 (mtp) cc_final: 0.8613 (mtp) REVERT: J 386 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8316 (mm-30) REVERT: J 764 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8731 (ttt-90) REVERT: J 1165 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: K 62 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8035 (tm-30) REVERT: L 137 TYR cc_start: 0.6778 (t80) cc_final: 0.6507 (t80) REVERT: L 546 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8509 (p0) REVERT: A 20 LYS cc_start: 0.9252 (mmmm) cc_final: 0.9035 (mmmm) REVERT: A 27 GLU cc_start: 0.8145 (tp30) cc_final: 0.7848 (tp30) REVERT: A 72 ARG cc_start: 0.9091 (ptp-110) cc_final: 0.8659 (ptt-90) REVERT: A 73 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8681 (mp10) REVERT: B 14 GLU cc_start: 0.9087 (tt0) cc_final: 0.8810 (tt0) REVERT: B 20 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9081 (mtmm) REVERT: B 28 LYS cc_start: 0.9271 (mtpt) cc_final: 0.8868 (mmmm) REVERT: B 31 GLU cc_start: 0.8907 (pt0) cc_final: 0.8381 (pt0) REVERT: B 33 VAL cc_start: 0.9295 (m) cc_final: 0.9082 (p) REVERT: B 46 ASP cc_start: 0.8936 (m-30) cc_final: 0.8672 (m-30) REVERT: B 51 PHE cc_start: 0.8692 (t80) cc_final: 0.8359 (t80) REVERT: B 53 MET cc_start: 0.8846 (tpp) cc_final: 0.8382 (tpp) REVERT: B 59 GLU cc_start: 0.8636 (mp0) cc_final: 0.8414 (mp0) REVERT: B 66 ASP cc_start: 0.7687 (m-30) cc_final: 0.7321 (t0) REVERT: B 69 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8176 (ttp-170) REVERT: C 28 LYS cc_start: 0.9251 (tppt) cc_final: 0.8931 (tppt) REVERT: C 59 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7833 (mp0) REVERT: D 27 GLU cc_start: 0.8793 (pm20) cc_final: 0.8026 (tm-30) REVERT: D 28 LYS cc_start: 0.9508 (mmpt) cc_final: 0.9233 (mmpt) REVERT: D 31 GLU cc_start: 0.9307 (pt0) cc_final: 0.8874 (pt0) outliers start: 115 outliers final: 66 residues processed: 401 average time/residue: 0.5142 time to fit residues: 328.7638 Evaluate side-chains 376 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 294 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 371 ARG Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 164 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 299 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 811 ASN J 365 GLN J 651 HIS C 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.055598 restraints weight = 68186.294| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.55 r_work: 0.2662 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30746 Z= 0.195 Angle : 0.587 8.337 42037 Z= 0.309 Chirality : 0.041 0.163 4806 Planarity : 0.004 0.049 5039 Dihedral : 18.020 179.904 5221 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.19 % Allowed : 20.81 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3478 helix: 1.54 (0.13), residues: 1566 sheet: -0.62 (0.25), residues: 373 loop : -0.92 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS G 23 PHE 0.020 0.002 PHE D 51 TYR 0.016 0.001 TYR G 177 ARG 0.008 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 1421) hydrogen bonds : angle 4.35930 ( 3977) metal coordination : bond 0.00837 ( 8) metal coordination : angle 3.21961 ( 12) covalent geometry : bond 0.00457 (30738) covalent geometry : angle 0.58421 (42025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 308 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: H 19 VAL cc_start: 0.6031 (OUTLIER) cc_final: 0.5819 (t) REVERT: H 218 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8154 (mtm-85) REVERT: I 69 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: I 105 TYR cc_start: 0.8420 (m-10) cc_final: 0.8194 (m-10) REVERT: I 165 HIS cc_start: 0.8798 (t-170) cc_final: 0.8594 (t-90) REVERT: I 370 MET cc_start: 0.8969 (mmm) cc_final: 0.8591 (mmm) REVERT: I 592 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8434 (ptm160) REVERT: I 637 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7679 (ptt-90) REVERT: I 878 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8455 (p) REVERT: I 1025 PHE cc_start: 0.7053 (t80) cc_final: 0.6638 (t80) REVERT: I 1028 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8767 (mmtm) REVERT: I 1170 MET cc_start: 0.9219 (mmp) cc_final: 0.8984 (mmm) REVERT: I 1304 MET cc_start: 0.9379 (tpt) cc_final: 0.9106 (tpp) REVERT: J 53 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7770 (tpt170) REVERT: J 160 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7951 (mt) REVERT: J 227 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8218 (t80) REVERT: J 330 MET cc_start: 0.8964 (mtp) cc_final: 0.8581 (mtp) REVERT: J 386 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: J 764 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8741 (ttt-90) REVERT: J 1165 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: K 62 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8054 (tm-30) REVERT: L 137 TYR cc_start: 0.6755 (t80) cc_final: 0.6461 (t80) REVERT: L 546 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8504 (p0) REVERT: A 20 LYS cc_start: 0.9283 (mmmm) cc_final: 0.9074 (mmmm) REVERT: A 72 ARG cc_start: 0.9065 (ptp-110) cc_final: 0.8775 (ptp-170) REVERT: A 73 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8624 (mp10) REVERT: B 14 GLU cc_start: 0.9103 (tt0) cc_final: 0.8802 (tt0) REVERT: B 20 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9057 (mtmm) REVERT: B 46 ASP cc_start: 0.8941 (m-30) cc_final: 0.8605 (m-30) REVERT: B 53 MET cc_start: 0.8862 (tpp) cc_final: 0.8379 (tpp) REVERT: B 59 GLU cc_start: 0.8658 (mp0) cc_final: 0.8289 (mp0) REVERT: B 66 ASP cc_start: 0.7692 (m-30) cc_final: 0.7313 (t0) REVERT: B 69 ARG cc_start: 0.8735 (ttp80) cc_final: 0.8164 (ttp-170) REVERT: D 27 GLU cc_start: 0.8750 (pm20) cc_final: 0.8035 (tm-30) REVERT: D 28 LYS cc_start: 0.9507 (mmpt) cc_final: 0.9203 (mmpt) REVERT: D 31 GLU cc_start: 0.9276 (pt0) cc_final: 0.8824 (pt0) outliers start: 125 outliers final: 74 residues processed: 408 average time/residue: 0.4529 time to fit residues: 290.1233 Evaluate side-chains 386 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 296 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 371 ARG Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 52 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 220 optimal weight: 0.0010 chunk 256 optimal weight: 0.8980 chunk 234 optimal weight: 0.0020 chunk 156 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 651 HIS C 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058277 restraints weight = 68595.523| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.59 r_work: 0.2725 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30746 Z= 0.112 Angle : 0.544 9.522 42037 Z= 0.287 Chirality : 0.039 0.149 4806 Planarity : 0.004 0.046 5039 Dihedral : 17.820 178.503 5221 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.15 % Allowed : 22.32 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3478 helix: 1.68 (0.13), residues: 1565 sheet: -0.62 (0.26), residues: 355 loop : -0.89 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 43 HIS 0.004 0.001 HIS I1070 PHE 0.030 0.001 PHE B 51 TYR 0.020 0.001 TYR J 679 ARG 0.008 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 1421) hydrogen bonds : angle 4.20223 ( 3977) metal coordination : bond 0.00383 ( 8) metal coordination : angle 2.28802 ( 12) covalent geometry : bond 0.00252 (30738) covalent geometry : angle 0.54226 (42025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 315 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: H 51 MET cc_start: 0.9095 (mmm) cc_final: 0.8819 (mmm) REVERT: H 95 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8668 (ttmm) REVERT: H 218 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8104 (mtm-85) REVERT: I 69 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8625 (pt0) REVERT: I 105 TYR cc_start: 0.8398 (m-10) cc_final: 0.8089 (m-10) REVERT: I 878 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8286 (p) REVERT: I 958 LYS cc_start: 0.8960 (tttp) cc_final: 0.8687 (ttpp) REVERT: I 1025 PHE cc_start: 0.6963 (t80) cc_final: 0.6687 (t80) REVERT: I 1027 LYS cc_start: 0.9190 (mttt) cc_final: 0.8945 (mmmt) REVERT: I 1028 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8770 (mmtm) REVERT: I 1170 MET cc_start: 0.9183 (mmp) cc_final: 0.8948 (mmm) REVERT: I 1304 MET cc_start: 0.9328 (tpt) cc_final: 0.9043 (tpp) REVERT: J 53 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7678 (tpt170) REVERT: J 160 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7877 (mt) REVERT: J 180 MET cc_start: 0.8558 (ttt) cc_final: 0.8356 (ttt) REVERT: J 227 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.7894 (t80) REVERT: J 330 MET cc_start: 0.8915 (mtp) cc_final: 0.8527 (mtp) REVERT: J 386 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: J 764 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8641 (ttt-90) REVERT: J 1165 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: J 1275 LEU cc_start: 0.7938 (mp) cc_final: 0.7699 (tp) REVERT: K 61 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7955 (t0) REVERT: K 62 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7972 (tm-30) REVERT: K 65 ASP cc_start: 0.8951 (p0) cc_final: 0.8721 (p0) REVERT: K 74 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8128 (mm-30) REVERT: L 485 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: A 27 GLU cc_start: 0.8592 (tp30) cc_final: 0.7801 (tp30) REVERT: A 31 GLU cc_start: 0.9164 (tt0) cc_final: 0.8889 (pt0) REVERT: A 72 ARG cc_start: 0.9080 (ptp-110) cc_final: 0.8842 (ptp-170) REVERT: B 12 ARG cc_start: 0.8922 (ttt180) cc_final: 0.8587 (ttp80) REVERT: B 14 GLU cc_start: 0.9065 (tt0) cc_final: 0.8723 (tt0) REVERT: B 46 ASP cc_start: 0.8949 (m-30) cc_final: 0.8616 (m-30) REVERT: B 53 MET cc_start: 0.8788 (tpp) cc_final: 0.8325 (tpp) REVERT: B 59 GLU cc_start: 0.8632 (mp0) cc_final: 0.8167 (mp0) REVERT: B 66 ASP cc_start: 0.7681 (m-30) cc_final: 0.7208 (t0) REVERT: B 69 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8014 (ttp-170) REVERT: C 23 MET cc_start: 0.8907 (mmm) cc_final: 0.8550 (mmm) REVERT: C 58 LEU cc_start: 0.8493 (tp) cc_final: 0.8194 (tp) REVERT: C 73 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8285 (mm-40) REVERT: D 27 GLU cc_start: 0.8653 (pm20) cc_final: 0.7937 (tm-30) REVERT: D 66 ASP cc_start: 0.8918 (t70) cc_final: 0.8699 (t70) outliers start: 94 outliers final: 49 residues processed: 394 average time/residue: 0.4590 time to fit residues: 281.4777 Evaluate side-chains 365 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 304 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 242 optimal weight: 9.9990 chunk 173 optimal weight: 0.0870 chunk 227 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 chunk 335 optimal weight: 0.9990 chunk 270 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 overall best weight: 3.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 798 GLN I 811 ASN J 651 HIS C 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055601 restraints weight = 69010.867| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.58 r_work: 0.2665 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30746 Z= 0.217 Angle : 0.604 9.715 42037 Z= 0.316 Chirality : 0.042 0.156 4806 Planarity : 0.004 0.042 5039 Dihedral : 17.889 178.714 5221 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.46 % Allowed : 22.15 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3478 helix: 1.64 (0.13), residues: 1567 sheet: -0.64 (0.25), residues: 396 loop : -0.82 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 43 HIS 0.005 0.001 HIS G 23 PHE 0.034 0.002 PHE B 51 TYR 0.017 0.001 TYR L 143 ARG 0.009 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 1421) hydrogen bonds : angle 4.27245 ( 3977) metal coordination : bond 0.00872 ( 8) metal coordination : angle 2.92122 ( 12) covalent geometry : bond 0.00511 (30738) covalent geometry : angle 0.60163 (42025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 306 time to evaluate : 4.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 283 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: H 95 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8660 (ttmm) REVERT: H 218 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8122 (mtm-85) REVERT: I 69 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8561 (pt0) REVERT: I 562 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: I 592 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8419 (ptm160) REVERT: I 637 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7682 (ptt-90) REVERT: I 878 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8482 (p) REVERT: I 1025 PHE cc_start: 0.7131 (t80) cc_final: 0.6789 (t80) REVERT: I 1028 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8771 (mmtm) REVERT: I 1170 MET cc_start: 0.9215 (mmp) cc_final: 0.8963 (mmm) REVERT: I 1304 MET cc_start: 0.9385 (tpt) cc_final: 0.9116 (tpp) REVERT: J 53 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7802 (tpt170) REVERT: J 227 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8170 (t80) REVERT: J 330 MET cc_start: 0.8945 (mtp) cc_final: 0.8576 (mtp) REVERT: J 386 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: J 764 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8718 (ttt-90) REVERT: J 1165 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: K 62 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7993 (tm-30) REVERT: L 485 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8469 (mp0) REVERT: L 546 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8543 (p0) REVERT: A 27 GLU cc_start: 0.8619 (tp30) cc_final: 0.7753 (tp30) REVERT: A 31 GLU cc_start: 0.9161 (tt0) cc_final: 0.8883 (pt0) REVERT: A 72 ARG cc_start: 0.9026 (ptp-110) cc_final: 0.8400 (ptt-90) REVERT: B 6 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8208 (tppt) REVERT: B 14 GLU cc_start: 0.9099 (tt0) cc_final: 0.8768 (tt0) REVERT: B 46 ASP cc_start: 0.8935 (m-30) cc_final: 0.8574 (m-30) REVERT: B 53 MET cc_start: 0.8831 (tpp) cc_final: 0.8132 (tpp) REVERT: B 59 GLU cc_start: 0.8677 (mp0) cc_final: 0.8345 (mp0) REVERT: B 66 ASP cc_start: 0.7829 (m-30) cc_final: 0.7404 (t0) REVERT: B 69 ARG cc_start: 0.8924 (ttp80) cc_final: 0.8489 (ttp-170) REVERT: C 23 MET cc_start: 0.9009 (mmm) cc_final: 0.8585 (mmm) REVERT: D 27 GLU cc_start: 0.8681 (pm20) cc_final: 0.7935 (tm-30) REVERT: D 28 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9169 (mmmt) REVERT: D 31 GLU cc_start: 0.9264 (pt0) cc_final: 0.8813 (pt0) REVERT: D 73 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8222 (tm-30) outliers start: 103 outliers final: 73 residues processed: 394 average time/residue: 0.6508 time to fit residues: 412.8809 Evaluate side-chains 384 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 297 time to evaluate : 7.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 281 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 489 ASN J 651 HIS C 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.083782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.056864 restraints weight = 69775.825| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.52 r_work: 0.2709 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30746 Z= 0.142 Angle : 0.584 11.035 42037 Z= 0.305 Chirality : 0.040 0.176 4806 Planarity : 0.004 0.042 5039 Dihedral : 17.848 178.315 5221 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.39 % Allowed : 22.75 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3478 helix: 1.70 (0.13), residues: 1560 sheet: -0.62 (0.25), residues: 376 loop : -0.81 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 43 HIS 0.003 0.001 HIS G 23 PHE 0.054 0.002 PHE B 51 TYR 0.023 0.001 TYR L 137 ARG 0.010 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1421) hydrogen bonds : angle 4.24808 ( 3977) metal coordination : bond 0.00548 ( 8) metal coordination : angle 2.54500 ( 12) covalent geometry : bond 0.00333 (30738) covalent geometry : angle 0.58272 (42025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 304 time to evaluate : 5.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8209 (mp10) cc_final: 0.7968 (mp10) REVERT: G 283 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: H 51 MET cc_start: 0.9053 (mmm) cc_final: 0.8779 (mmm) REVERT: H 95 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8729 (ttmm) REVERT: H 218 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8207 (mtm-85) REVERT: I 69 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: I 562 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: I 592 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8553 (ptm160) REVERT: I 637 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: I 878 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8589 (p) REVERT: I 1025 PHE cc_start: 0.7087 (t80) cc_final: 0.6844 (t80) REVERT: I 1028 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8775 (mmtm) REVERT: I 1170 MET cc_start: 0.9218 (mmp) cc_final: 0.8985 (mmm) REVERT: I 1304 MET cc_start: 0.9411 (tpt) cc_final: 0.9152 (tpp) REVERT: J 53 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7716 (tpt170) REVERT: J 160 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8060 (mt) REVERT: J 227 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8255 (t80) REVERT: J 330 MET cc_start: 0.8848 (mtp) cc_final: 0.8540 (mtp) REVERT: J 386 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: J 697 MET cc_start: 0.8251 (ttp) cc_final: 0.8036 (ttp) REVERT: J 764 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8835 (ttt-90) REVERT: J 822 MET cc_start: 0.8735 (mmm) cc_final: 0.8277 (mmm) REVERT: J 1165 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: J 1275 LEU cc_start: 0.7985 (mp) cc_final: 0.7748 (tp) REVERT: K 11 GLU cc_start: 0.9056 (pt0) cc_final: 0.8791 (pp20) REVERT: K 61 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8298 (t0) REVERT: K 62 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7981 (tm-30) REVERT: K 74 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8223 (mm-30) REVERT: L 485 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: A 27 GLU cc_start: 0.8632 (tp30) cc_final: 0.7745 (tp30) REVERT: A 31 GLU cc_start: 0.9105 (tt0) cc_final: 0.8870 (pt0) REVERT: A 51 PHE cc_start: 0.8319 (m-80) cc_final: 0.8070 (t80) REVERT: A 69 ARG cc_start: 0.9200 (mtm110) cc_final: 0.8889 (mtp180) REVERT: A 72 ARG cc_start: 0.8985 (ptp-110) cc_final: 0.8352 (ptt-90) REVERT: B 14 GLU cc_start: 0.9050 (tt0) cc_final: 0.8612 (tt0) REVERT: B 20 LYS cc_start: 0.9196 (mtmm) cc_final: 0.8991 (mtmm) REVERT: B 46 ASP cc_start: 0.8876 (m-30) cc_final: 0.8510 (m-30) REVERT: B 53 MET cc_start: 0.8810 (tpp) cc_final: 0.8304 (tpp) REVERT: B 59 GLU cc_start: 0.8638 (mp0) cc_final: 0.8324 (mp0) REVERT: B 66 ASP cc_start: 0.7870 (m-30) cc_final: 0.7376 (t0) REVERT: B 69 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8504 (ttp-170) REVERT: C 23 MET cc_start: 0.9043 (mmm) cc_final: 0.8633 (mmm) REVERT: D 26 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (t) REVERT: D 27 GLU cc_start: 0.8667 (pm20) cc_final: 0.8133 (tm-30) REVERT: D 28 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9258 (mmmt) outliers start: 101 outliers final: 72 residues processed: 390 average time/residue: 0.6213 time to fit residues: 390.7627 Evaluate side-chains 385 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 297 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 54 optimal weight: 0.0770 chunk 354 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 298 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 355 optimal weight: 8.9990 overall best weight: 2.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 965 GLN J 651 HIS C 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.083225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056059 restraints weight = 69295.528| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.54 r_work: 0.2686 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30746 Z= 0.180 Angle : 0.605 12.564 42037 Z= 0.315 Chirality : 0.041 0.256 4806 Planarity : 0.004 0.041 5039 Dihedral : 17.843 178.204 5221 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.46 % Allowed : 22.92 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3478 helix: 1.62 (0.13), residues: 1570 sheet: -0.64 (0.25), residues: 376 loop : -0.81 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 43 HIS 0.004 0.001 HIS G 23 PHE 0.051 0.002 PHE B 51 TYR 0.023 0.001 TYR L 143 ARG 0.011 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1421) hydrogen bonds : angle 4.27132 ( 3977) metal coordination : bond 0.00716 ( 8) metal coordination : angle 2.74729 ( 12) covalent geometry : bond 0.00422 (30738) covalent geometry : angle 0.60322 (42025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 299 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8204 (mp10) cc_final: 0.7944 (mp10) REVERT: G 283 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: H 95 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8709 (ttmm) REVERT: H 218 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8178 (mtm-85) REVERT: I 57 PHE cc_start: 0.8624 (t80) cc_final: 0.8201 (t80) REVERT: I 69 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: I 562 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: I 592 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8479 (ptm160) REVERT: I 637 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7683 (ptt-90) REVERT: I 878 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8573 (p) REVERT: I 1025 PHE cc_start: 0.7219 (t80) cc_final: 0.6979 (t80) REVERT: I 1028 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8760 (mmtm) REVERT: I 1170 MET cc_start: 0.9232 (mmp) cc_final: 0.8990 (mmm) REVERT: I 1304 MET cc_start: 0.9420 (tpt) cc_final: 0.9160 (tpp) REVERT: J 53 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7801 (tpt170) REVERT: J 160 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8032 (mt) REVERT: J 227 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8266 (t80) REVERT: J 330 MET cc_start: 0.8876 (mtp) cc_final: 0.8523 (mtp) REVERT: J 386 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8314 (mm-30) REVERT: J 764 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8770 (ttt-90) REVERT: J 1165 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: K 11 GLU cc_start: 0.9125 (pt0) cc_final: 0.8834 (pp20) REVERT: K 62 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8149 (tm-30) REVERT: K 74 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8196 (mm-30) REVERT: L 485 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: L 546 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8518 (p0) REVERT: A 27 GLU cc_start: 0.8654 (tp30) cc_final: 0.7747 (tp30) REVERT: A 31 GLU cc_start: 0.9090 (tt0) cc_final: 0.8763 (pt0) REVERT: A 51 PHE cc_start: 0.8381 (m-80) cc_final: 0.8116 (t80) REVERT: B 14 GLU cc_start: 0.9076 (tt0) cc_final: 0.8642 (tt0) REVERT: B 36 ASP cc_start: 0.7789 (t0) cc_final: 0.6177 (t0) REVERT: B 39 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: B 46 ASP cc_start: 0.8867 (m-30) cc_final: 0.8480 (m-30) REVERT: B 53 MET cc_start: 0.8844 (tpp) cc_final: 0.8352 (tpp) REVERT: B 59 GLU cc_start: 0.8685 (mp0) cc_final: 0.8394 (mp0) REVERT: B 66 ASP cc_start: 0.7838 (m-30) cc_final: 0.7363 (t0) REVERT: B 69 ARG cc_start: 0.8999 (ttp80) cc_final: 0.8630 (ttp-170) REVERT: C 9 GLU cc_start: 0.8309 (tp30) cc_final: 0.8101 (tp30) REVERT: C 23 MET cc_start: 0.8973 (mmm) cc_final: 0.8524 (mmm) REVERT: C 28 LYS cc_start: 0.9277 (tppt) cc_final: 0.9061 (tppt) REVERT: D 27 GLU cc_start: 0.8655 (pm20) cc_final: 0.8112 (tm-30) REVERT: D 28 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9241 (mmmt) outliers start: 103 outliers final: 80 residues processed: 385 average time/residue: 0.4508 time to fit residues: 274.3219 Evaluate side-chains 390 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 294 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 965 GLN Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 351 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN J 651 HIS C 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055460 restraints weight = 68686.201| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.48 r_work: 0.2671 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30746 Z= 0.217 Angle : 0.635 11.761 42037 Z= 0.329 Chirality : 0.042 0.242 4806 Planarity : 0.004 0.046 5039 Dihedral : 17.863 178.295 5221 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.39 % Allowed : 23.09 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3478 helix: 1.58 (0.13), residues: 1574 sheet: -0.68 (0.25), residues: 395 loop : -0.82 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 43 HIS 0.004 0.001 HIS G 23 PHE 0.047 0.002 PHE B 51 TYR 0.020 0.001 TYR L 143 ARG 0.011 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1421) hydrogen bonds : angle 4.31418 ( 3977) metal coordination : bond 0.00861 ( 8) metal coordination : angle 3.01095 ( 12) covalent geometry : bond 0.00509 (30738) covalent geometry : angle 0.63307 (42025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6956 Ramachandran restraints generated. 3478 Oldfield, 0 Emsley, 3478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 299 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8355 (mp10) cc_final: 0.8089 (mp10) REVERT: G 283 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: H 95 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8705 (ttmm) REVERT: H 218 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8304 (mtm-85) REVERT: I 57 PHE cc_start: 0.8706 (t80) cc_final: 0.8378 (t80) REVERT: I 69 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8593 (pt0) REVERT: I 562 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: I 592 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8546 (ptm160) REVERT: I 637 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7904 (ptt-90) REVERT: I 878 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8674 (p) REVERT: I 1025 PHE cc_start: 0.7335 (t80) cc_final: 0.7046 (t80) REVERT: I 1304 MET cc_start: 0.9525 (tpt) cc_final: 0.9269 (tpp) REVERT: J 53 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7911 (tpt170) REVERT: J 160 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8175 (mt) REVERT: J 227 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8370 (t80) REVERT: J 330 MET cc_start: 0.9026 (mtp) cc_final: 0.8718 (mtp) REVERT: J 386 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: J 764 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8876 (ttt-90) REVERT: J 822 MET cc_start: 0.8931 (mmm) cc_final: 0.8438 (mmm) REVERT: J 1165 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: K 62 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8255 (tm-30) REVERT: K 74 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8150 (mm-30) REVERT: L 485 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: L 546 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8623 (p0) REVERT: L 567 MET cc_start: 0.8137 (ptp) cc_final: 0.7935 (ptp) REVERT: A 27 GLU cc_start: 0.8694 (tp30) cc_final: 0.7796 (tp30) REVERT: A 31 GLU cc_start: 0.9143 (tt0) cc_final: 0.8814 (pt0) REVERT: A 45 ARG cc_start: 0.9132 (ttp80) cc_final: 0.8884 (ttp80) REVERT: A 51 PHE cc_start: 0.8478 (m-80) cc_final: 0.8181 (t80) REVERT: A 72 ARG cc_start: 0.9190 (ptp-170) cc_final: 0.8702 (ptt-90) REVERT: B 14 GLU cc_start: 0.9163 (tt0) cc_final: 0.8738 (tt0) REVERT: B 20 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8711 (ptpp) REVERT: B 36 ASP cc_start: 0.7940 (t0) cc_final: 0.6428 (t0) REVERT: B 37 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8517 (tptt) REVERT: B 39 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: B 46 ASP cc_start: 0.8913 (m-30) cc_final: 0.8501 (m-30) REVERT: B 53 MET cc_start: 0.8924 (tpp) cc_final: 0.8604 (tpt) REVERT: B 59 GLU cc_start: 0.8719 (mp0) cc_final: 0.8439 (mp0) REVERT: B 66 ASP cc_start: 0.7902 (m-30) cc_final: 0.7319 (t0) REVERT: B 69 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8590 (ttp-170) REVERT: C 9 GLU cc_start: 0.8429 (tp30) cc_final: 0.8192 (tp30) REVERT: C 23 MET cc_start: 0.9076 (mmm) cc_final: 0.8653 (mmm) REVERT: D 27 GLU cc_start: 0.8769 (pm20) cc_final: 0.8074 (tm-30) REVERT: D 28 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9250 (mmmt) outliers start: 101 outliers final: 82 residues processed: 383 average time/residue: 0.4540 time to fit residues: 274.3381 Evaluate side-chains 393 residues out of total 2988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 295 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 218 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 965 GLN Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 764 ARG Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 546 ASP Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 286 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 349 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN J 651 HIS C 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.082721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.055634 restraints weight = 69123.572| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.52 r_work: 0.2675 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30746 Z= 0.191 Angle : 0.623 12.139 42037 Z= 0.324 Chirality : 0.042 0.226 4806 Planarity : 0.004 0.047 5039 Dihedral : 17.860 178.218 5221 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.36 % Allowed : 23.22 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3478 helix: 1.58 (0.13), residues: 1574 sheet: -0.69 (0.25), residues: 385 loop : -0.82 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 43 HIS 0.004 0.001 HIS G 23 PHE 0.046 0.002 PHE B 51 TYR 0.020 0.001 TYR L 143 ARG 0.011 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1421) hydrogen bonds : angle 4.30978 ( 3977) metal coordination : bond 0.00780 ( 8) metal coordination : angle 2.96487 ( 12) covalent geometry : bond 0.00448 (30738) covalent geometry : angle 0.62117 (42025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18625.71 seconds wall clock time: 326 minutes 41.47 seconds (19601.47 seconds total)