Starting phenix.real_space_refine on Wed Sep 25 07:23:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/09_2024/7ozp_13131.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/09_2024/7ozp_13131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/09_2024/7ozp_13131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/09_2024/7ozp_13131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/09_2024/7ozp_13131.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozp_13131/09_2024/7ozp_13131.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.921 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 312 5.16 5 C 34364 2.51 5 N 9406 2.21 5 O 10238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54330 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8233 Classifications: {'peptide': 1033} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 989} Chain breaks: 6 Chain: "B" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8179 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 48, 'TRANS': 974} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17106 SG CYS C 88 119.305 60.478 14.511 1.00 88.48 S ATOM 17119 SG CYS C 90 116.492 62.194 12.536 1.00 96.81 S ATOM 17154 SG CYS C 94 116.874 58.802 11.711 1.00 89.88 S ATOM 17176 SG CYS C 97 115.785 59.110 15.021 1.00 85.73 S ATOM 24473 SG CYS I 17 25.152 44.936 91.935 1.00 97.63 S ATOM 24497 SG CYS I 20 23.998 47.782 89.837 1.00101.80 S ATOM 24658 SG CYS I 39 26.162 48.418 93.021 1.00101.17 S ATOM 24683 SG CYS I 42 22.531 47.402 93.297 1.00102.57 S ATOM 25035 SG CYS I 86 53.095 13.145 84.921 1.00 81.20 S ATOM 25059 SG CYS I 89 50.741 11.122 82.631 1.00 81.91 S ATOM 25263 SG CYS I 114 53.180 13.804 81.203 1.00 72.52 S ATOM 25298 SG CYS I 119 50.104 14.726 83.149 1.00 76.54 S ATOM 25408 SG CYS J 7 103.144 37.532 35.444 1.00 36.75 S ATOM 25432 SG CYS J 10 106.829 36.631 34.766 1.00 32.02 S ATOM 25696 SG CYS J 44 104.876 34.936 37.576 1.00 30.26 S ATOM 25702 SG CYS J 45 104.176 34.153 33.929 1.00 37.06 S ATOM 26830 SG CYS L 19 69.481 57.081 14.225 1.00 97.39 S ATOM 26849 SG CYS L 22 70.139 55.504 10.860 1.00101.71 S ATOM 26966 SG CYS L 36 68.216 58.809 11.115 1.00100.08 S ATOM 26992 SG CYS L 39 66.601 55.526 12.092 1.00102.43 S Restraints were copied for chains: U, T, V, S, M, P, O, W, N, X, Q, R Time building chain proxies: 36.82, per 1000 atoms: 0.68 Number of scatterers: 54330 At special positions: 0 Unit cell: (162.583, 223.041, 142.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 312 16.00 O 10238 8.00 N 9406 7.00 C 34364 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: 11.04 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 90 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 97 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 88 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 17 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 42 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 20 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 39 " pdb=" ZN U 202 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 119 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 114 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 86 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 89 " pdb=" ZN V 101 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 44 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 10 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 7 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 22 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 36 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 39 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 19 " Number of angles added : 60 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12796 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 78 sheets defined 39.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.812A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.638A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.655A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.680A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.055A pdb=" N ASP A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.535A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.867A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.507A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.720A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.972A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.521A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1153 No H-bonds generated for 'chain 'A' and resid 1151 through 1153' Processing helix chain 'A' and resid 1154 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.588A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 3.520A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1281 through 1295 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.937A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.736A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.617A pdb=" N CYS A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.304A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.520A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.580A pdb=" N ARG B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.664A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 removed outlier: 4.169A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.560A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 4.146A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.702A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.506A pdb=" N ARG B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.554A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.165A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.509A pdb=" N LEU B 505 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.694A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.630A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.862A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.991A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 657 " --> pdb=" O TRP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.949A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.685A pdb=" N LEU B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.904A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.550A pdb=" N ALA B 727 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 4.348A pdb=" N TYR B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.237A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.523A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1061 removed outlier: 3.650A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.787A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.702A pdb=" N LEU C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 240 through 271 removed outlier: 4.157A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 33 through 51 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.638A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.965A pdb=" N GLU D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.917A pdb=" N ASP D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.638A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.584A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.599A pdb=" N LYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.814A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.613A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.623A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.662A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 removed outlier: 4.293A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 removed outlier: 4.141A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.784A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.649A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.758A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.193A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 68 Processing helix chain 'K' and resid 82 through 115 removed outlier: 3.852A pdb=" N LYS K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 388 Processing helix chain 'M' and resid 395 through 397 No H-bonds generated for 'chain 'M' and resid 395 through 397' Processing helix chain 'M' and resid 398 through 409 removed outlier: 3.811A pdb=" N GLY M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 439 Processing helix chain 'M' and resid 508 through 519 Processing helix chain 'M' and resid 520 through 525 Processing helix chain 'M' and resid 538 through 549 removed outlier: 3.638A pdb=" N THR M 543 " --> pdb=" O GLN M 539 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA M 544 " --> pdb=" O ASP M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 556 through 566 removed outlier: 3.655A pdb=" N ASN M 562 " --> pdb=" O GLY M 558 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE M 566 " --> pdb=" O ASN M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 596 removed outlier: 3.680A pdb=" N LEU M 594 " --> pdb=" O GLN M 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE M 595 " --> pdb=" O ILE M 591 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 616 removed outlier: 4.054A pdb=" N ASP M 614 " --> pdb=" O PRO M 610 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 641 through 646 Processing helix chain 'M' and resid 651 through 660 Processing helix chain 'M' and resid 661 through 684 removed outlier: 3.534A pdb=" N THR M 665 " --> pdb=" O GLY M 661 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE M 682 " --> pdb=" O ASN M 678 " (cutoff:3.500A) Processing helix chain 'M' and resid 688 through 693 removed outlier: 3.868A pdb=" N SER M 692 " --> pdb=" O GLY M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 695 through 722 Processing helix chain 'M' and resid 732 through 760 Processing helix chain 'M' and resid 764 through 773 Processing helix chain 'M' and resid 777 through 786 Processing helix chain 'M' and resid 832 through 869 removed outlier: 3.507A pdb=" N PHE M 837 " --> pdb=" O PRO M 833 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA M 855 " --> pdb=" O ALA M 851 " (cutoff:3.500A) Processing helix chain 'M' and resid 890 through 894 Processing helix chain 'M' and resid 914 through 921 Processing helix chain 'M' and resid 926 through 934 Processing helix chain 'M' and resid 935 through 945 removed outlier: 3.719A pdb=" N ASN M 945 " --> pdb=" O ASP M 941 " (cutoff:3.500A) Processing helix chain 'M' and resid 945 through 970 removed outlier: 3.973A pdb=" N GLN M 949 " --> pdb=" O ASN M 945 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG M 967 " --> pdb=" O ARG M 963 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL M 968 " --> pdb=" O GLU M 964 " (cutoff:3.500A) Processing helix chain 'M' and resid 982 through 995 Processing helix chain 'M' and resid 1005 through 1020 removed outlier: 3.520A pdb=" N VAL M1009 " --> pdb=" O HIS M1005 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL M1010 " --> pdb=" O PRO M1006 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS M1018 " --> pdb=" O LYS M1014 " (cutoff:3.500A) Processing helix chain 'M' and resid 1027 through 1038 Processing helix chain 'M' and resid 1038 through 1049 Processing helix chain 'M' and resid 1050 through 1057 Processing helix chain 'M' and resid 1061 through 1080 Processing helix chain 'M' and resid 1086 through 1100 Proline residue: M1098 - end of helix Processing helix chain 'M' and resid 1120 through 1129 Processing helix chain 'M' and resid 1145 through 1149 Processing helix chain 'M' and resid 1151 through 1153 No H-bonds generated for 'chain 'M' and resid 1151 through 1153' Processing helix chain 'M' and resid 1154 through 1162 Processing helix chain 'M' and resid 1165 through 1169 removed outlier: 3.588A pdb=" N VAL M1169 " --> pdb=" O THR M1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1165 through 1169' Processing helix chain 'M' and resid 1189 through 1199 removed outlier: 3.520A pdb=" N ASN M1194 " --> pdb=" O GLN M1190 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL M1195 " --> pdb=" O GLU M1191 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET M1199 " --> pdb=" O VAL M1195 " (cutoff:3.500A) Processing helix chain 'M' and resid 1217 through 1225 Processing helix chain 'M' and resid 1227 through 1240 Processing helix chain 'M' and resid 1262 through 1267 Processing helix chain 'M' and resid 1281 through 1295 Processing helix chain 'M' and resid 1342 through 1348 removed outlier: 3.937A pdb=" N SER M1348 " --> pdb=" O MET M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1361 through 1369 Processing helix chain 'M' and resid 1370 through 1389 removed outlier: 3.736A pdb=" N LYS M1376 " --> pdb=" O GLU M1372 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP M1389 " --> pdb=" O VAL M1385 " (cutoff:3.500A) Processing helix chain 'M' and resid 1394 through 1406 Processing helix chain 'M' and resid 1476 through 1481 removed outlier: 3.617A pdb=" N CYS M1480 " --> pdb=" O ASP M1476 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 37 removed outlier: 4.304A pdb=" N GLN N 23 " --> pdb=" O PRO N 19 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU N 24 " --> pdb=" O ASP N 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE N 30 " --> pdb=" O CYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 53 removed outlier: 3.520A pdb=" N SER N 46 " --> pdb=" O GLN N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 61 Processing helix chain 'N' and resid 109 through 117 removed outlier: 3.580A pdb=" N ARG N 114 " --> pdb=" O PRO N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 174 Processing helix chain 'N' and resid 248 through 253 Processing helix chain 'N' and resid 269 through 277 Processing helix chain 'N' and resid 280 through 289 removed outlier: 3.664A pdb=" N ILE N 284 " --> pdb=" O SER N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 310 removed outlier: 4.169A pdb=" N MET N 298 " --> pdb=" O ASP N 294 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET N 300 " --> pdb=" O GLU N 296 " (cutoff:3.500A) Proline residue: N 303 - end of helix removed outlier: 3.560A pdb=" N ASP N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU N 307 " --> pdb=" O PRO N 303 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA N 308 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL N 310 " --> pdb=" O ASP N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 324 removed outlier: 4.146A pdb=" N ARG N 324 " --> pdb=" O PHE N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 345 removed outlier: 3.701A pdb=" N ARG N 335 " --> pdb=" O THR N 331 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE N 336 " --> pdb=" O LYS N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 378 Processing helix chain 'N' and resid 387 through 389 No H-bonds generated for 'chain 'N' and resid 387 through 389' Processing helix chain 'N' and resid 395 through 426 removed outlier: 3.507A pdb=" N ARG N 405 " --> pdb=" O ALA N 401 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY N 406 " --> pdb=" O PHE N 402 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET N 407 " --> pdb=" O LEU N 403 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS N 421 " --> pdb=" O ILE N 417 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE N 422 " --> pdb=" O TYR N 418 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG N 425 " --> pdb=" O LYS N 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 435 removed outlier: 3.553A pdb=" N ALA N 434 " --> pdb=" O ASN N 430 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 451 removed outlier: 4.165A pdb=" N ILE N 440 " --> pdb=" O LYS N 436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU N 444 " --> pdb=" O ILE N 440 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER N 447 " --> pdb=" O GLY N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 474 through 483 Processing helix chain 'N' and resid 490 through 496 Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.508A pdb=" N LEU N 505 " --> pdb=" O HIS N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 548 removed outlier: 3.694A pdb=" N GLU N 546 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU N 547 " --> pdb=" O GLU N 543 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP N 548 " --> pdb=" O PHE N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 562 removed outlier: 3.630A pdb=" N ALA N 562 " --> pdb=" O ALA N 559 " (cutoff:3.500A) Processing helix chain 'N' and resid 579 through 593 removed outlier: 3.863A pdb=" N LEU N 583 " --> pdb=" O ASP N 579 " (cutoff:3.500A) Processing helix chain 'N' and resid 607 through 609 No H-bonds generated for 'chain 'N' and resid 607 through 609' Processing helix chain 'N' and resid 636 through 645 Processing helix chain 'N' and resid 652 through 659 removed outlier: 3.991A pdb=" N LEU N 656 " --> pdb=" O SER N 652 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL N 657 " --> pdb=" O TRP N 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 672 removed outlier: 3.948A pdb=" N THR N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 678 through 684 removed outlier: 3.685A pdb=" N LEU N 682 " --> pdb=" O THR N 678 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU N 684 " --> pdb=" O ASP N 680 " (cutoff:3.500A) Processing helix chain 'N' and resid 699 through 704 Processing helix chain 'N' and resid 705 through 710 removed outlier: 3.904A pdb=" N ILE N 710 " --> pdb=" O VAL N 706 " (cutoff:3.500A) Processing helix chain 'N' and resid 718 through 732 removed outlier: 3.549A pdb=" N ALA N 727 " --> pdb=" O THR N 723 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS N 730 " --> pdb=" O SER N 726 " (cutoff:3.500A) Processing helix chain 'N' and resid 762 through 767 removed outlier: 4.347A pdb=" N TYR N 766 " --> pdb=" O ARG N 762 " (cutoff:3.500A) Processing helix chain 'N' and resid 798 through 803 Processing helix chain 'N' and resid 969 through 972 Processing helix chain 'N' and resid 977 through 994 removed outlier: 4.237A pdb=" N LEU N 981 " --> pdb=" O THR N 977 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1017 removed outlier: 3.524A pdb=" N ASP N1017 " --> pdb=" O ASN N1013 " (cutoff:3.500A) Processing helix chain 'N' and resid 1054 through 1061 removed outlier: 3.651A pdb=" N LYS N1058 " --> pdb=" O MET N1054 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 40 removed outlier: 3.786A pdb=" N ILE O 39 " --> pdb=" O ARG O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 71 removed outlier: 3.703A pdb=" N LEU O 68 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU O 70 " --> pdb=" O HIS O 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE O 71 " --> pdb=" O ARG O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 118 through 120 No H-bonds generated for 'chain 'O' and resid 118 through 120' Processing helix chain 'O' and resid 173 through 177 Processing helix chain 'O' and resid 240 through 271 removed outlier: 4.158A pdb=" N VAL O 245 " --> pdb=" O PRO O 241 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU O 246 " --> pdb=" O GLU O 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 28 Processing helix chain 'P' and resid 33 through 51 Processing helix chain 'P' and resid 58 through 71 Processing helix chain 'P' and resid 76 through 89 Processing helix chain 'P' and resid 93 through 104 removed outlier: 3.638A pdb=" N ALA P 98 " --> pdb=" O LYS P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 115 Processing helix chain 'P' and resid 115 through 122 removed outlier: 3.966A pdb=" N GLU P 119 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY P 120 " --> pdb=" O PRO P 116 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG P 121 " --> pdb=" O SER P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.917A pdb=" N ASP P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 25 removed outlier: 3.638A pdb=" N TYR Q 8 " --> pdb=" O GLU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.585A pdb=" N LEU Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP Q 34 " --> pdb=" O GLN Q 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 34' Processing helix chain 'Q' and resid 36 through 45 removed outlier: 3.599A pdb=" N LYS Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 98 removed outlier: 3.815A pdb=" N GLU Q 96 " --> pdb=" O GLN Q 92 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU Q 97 " --> pdb=" O ARG Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 121 removed outlier: 3.613A pdb=" N GLN Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 136 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'R' and resid 58 through 75 Processing helix chain 'R' and resid 88 through 100 Processing helix chain 'S' and resid 14 through 18 Processing helix chain 'S' and resid 21 through 34 removed outlier: 3.623A pdb=" N THR S 25 " --> pdb=" O ASN S 21 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR S 32 " --> pdb=" O GLN S 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 75 removed outlier: 3.663A pdb=" N SER U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 107 removed outlier: 4.293A pdb=" N ASP U 106 " --> pdb=" O ARG U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 26 removed outlier: 4.141A pdb=" N GLU V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA V 20 " --> pdb=" O ASN V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 39 removed outlier: 3.784A pdb=" N LEU V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 51 removed outlier: 3.648A pdb=" N MET V 48 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU V 49 " --> pdb=" O CYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.759A pdb=" N SER W 9 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 53 removed outlier: 4.194A pdb=" N ILE W 45 " --> pdb=" O THR W 41 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE W 46 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN W 49 " --> pdb=" O ILE W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 68 Processing helix chain 'W' and resid 82 through 115 removed outlier: 3.852A pdb=" N LYS W 110 " --> pdb=" O ARG W 106 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.994A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.125A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.519A pdb=" N CYS A 602 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AA8, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.921A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.374A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1320 through 1322 removed outlier: 3.758A pdb=" N LYS A1329 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.618A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.618A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.614A pdb=" N TYR B 84 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.528A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB7, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.746A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.532A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 233 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC2, first strand: chain 'B' and resid 572 through 573 removed outlier: 5.973A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.784A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.784A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC6, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.983A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 827 through 828 removed outlier: 4.840A pdb=" N CYS B 837 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP B 891 " --> pdb=" O CYS B 837 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY B 839 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.640A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD1, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.759A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.878A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD4, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.246A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 74 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 81 through 82 removed outlier: 4.056A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.873A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 83 through 92 removed outlier: 7.302A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 117 through 118 Processing sheet with id=AD9, first strand: chain 'H' and resid 101 through 102 removed outlier: 4.190A pdb=" N ARG H 111 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AE2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE3, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AE4, first strand: chain 'M' and resid 367 through 369 removed outlier: 5.994A pdb=" N THR M 368 " --> pdb=" O LEU M 484 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL M 378 " --> pdb=" O ARG M 475 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU M 477 " --> pdb=" O VAL M 378 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL M 380 " --> pdb=" O LEU M 477 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 389 through 393 removed outlier: 4.126A pdb=" N TYR M 418 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS M 449 " --> pdb=" O ALA M 416 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA M 416 " --> pdb=" O HIS M 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 554 through 555 Processing sheet with id=AE7, first strand: chain 'M' and resid 602 through 605 removed outlier: 3.519A pdb=" N CYS M 602 " --> pdb=" O VAL M 630 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL M 629 " --> pdb=" O ILE M 636 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 789 through 790 Processing sheet with id=AE9, first strand: chain 'M' and resid 872 through 873 Processing sheet with id=AF1, first strand: chain 'M' and resid 902 through 905 Processing sheet with id=AF2, first strand: chain 'M' and resid 1307 through 1310 removed outlier: 3.921A pdb=" N ILE M1335 " --> pdb=" O HIS M1310 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR M1358 " --> pdb=" O THR M1140 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 1243 through 1247 removed outlier: 4.374A pdb=" N LEU M1255 " --> pdb=" O LEU M1216 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN M1172 " --> pdb=" O GLU M1215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR U 54 " --> pdb=" O ILE M1175 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 1320 through 1322 removed outlier: 3.758A pdb=" N LYS M1329 " --> pdb=" O ILE M1321 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.618A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL S 66 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY S 57 " --> pdb=" O LEU M1475 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU M1473 " --> pdb=" O ILE S 59 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.618A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL S 66 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE S 54 " --> pdb=" O PRO S 69 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS S 71 " --> pdb=" O ASP S 52 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE S 75 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL S 48 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE S 77 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE S 46 " --> pdb=" O PHE S 77 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 65 through 67 removed outlier: 3.613A pdb=" N TYR N 84 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR N 84 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE N 133 " --> pdb=" O TYR N 84 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU N 86 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR N 131 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE N 88 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR N 129 " --> pdb=" O PHE N 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN N 90 " --> pdb=" O ASP N 127 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL N 126 " --> pdb=" O PHE N 148 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE N 148 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE N 128 " --> pdb=" O LYS N 146 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS N 146 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS N 130 " --> pdb=" O HIS N 144 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS N 144 " --> pdb=" O LYS N 130 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL N 132 " --> pdb=" O THR N 142 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR N 142 " --> pdb=" O VAL N 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 97 through 98 removed outlier: 3.529A pdb=" N SER N 106 " --> pdb=" O HIS N 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 185 through 187 Processing sheet with id=AG1, first strand: chain 'N' and resid 391 through 394 removed outlier: 3.745A pdb=" N ALA N 196 " --> pdb=" O ARG N 484 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 206 through 209 removed outlier: 3.532A pdb=" N TYR N 217 " --> pdb=" O MET N 239 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE N 235 " --> pdb=" O CYS N 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER N 233 " --> pdb=" O SER N 223 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP N 236 " --> pdb=" O THR N 259 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG4, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG5, first strand: chain 'N' and resid 572 through 573 removed outlier: 5.972A pdb=" N LYS N 566 " --> pdb=" O ILE N 612 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE N 614 " --> pdb=" O LYS N 566 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE N 568 " --> pdb=" O ILE N 614 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.783A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.783A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL N 907 " --> pdb=" O LYS X 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 759 through 760 Processing sheet with id=AG9, first strand: chain 'N' and resid 1025 through 1026 removed outlier: 6.983A pdb=" N VAL N 794 " --> pdb=" O GLY N 946 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN N 948 " --> pdb=" O VAL N 794 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET N 796 " --> pdb=" O GLN N 948 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE N 965 " --> pdb=" O ILE N 779 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE N 967 " --> pdb=" O ALA N 781 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE N1042 " --> pdb=" O ILE N 782 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 827 through 828 removed outlier: 4.840A pdb=" N CYS N 837 " --> pdb=" O LYS N 889 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP N 891 " --> pdb=" O CYS N 837 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY N 839 " --> pdb=" O ASP N 891 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 865 through 867 removed outlier: 3.639A pdb=" N ILE N 866 " --> pdb=" O THR N 894 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR N 894 " --> pdb=" O ILE N 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'N' and resid 956 through 957 Processing sheet with id=AH4, first strand: chain 'O' and resid 8 through 14 removed outlier: 6.758A pdb=" N LYS O 20 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU O 14 " --> pdb=" O ASN O 18 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN O 232 " --> pdb=" O VAL O 182 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL O 182 " --> pdb=" O ASN O 232 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU O 234 " --> pdb=" O ALA O 180 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 121 through 122 removed outlier: 6.878A pdb=" N GLU O 158 " --> pdb=" O ASN O 55 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN O 55 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG O 160 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS O 166 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE O 47 " --> pdb=" O LYS O 166 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY O 168 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE O 45 " --> pdb=" O GLY O 168 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 113 through 116 Processing sheet with id=AH7, first strand: chain 'Q' and resid 26 through 27 removed outlier: 4.246A pdb=" N ALA Q 63 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL Q 60 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL Q 74 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL Q 62 " --> pdb=" O MET Q 72 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG Q 101 " --> pdb=" O GLN Q 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU Q 128 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 81 through 82 removed outlier: 4.056A pdb=" N VAL Q 82 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Q' and resid 147 through 151 removed outlier: 3.874A pdb=" N GLU Q 147 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL Q 190 " --> pdb=" O MET Q 151 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 83 through 92 removed outlier: 7.302A pdb=" N PHE S 98 " --> pdb=" O THR S 90 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER S 105 " --> pdb=" O ILE S 157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA S 159 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER S 162 " --> pdb=" O ILE S 147 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE S 147 " --> pdb=" O SER S 162 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU S 83 " --> pdb=" O ILE S 147 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 117 through 118 Processing sheet with id=AI3, first strand: chain 'T' and resid 101 through 102 removed outlier: 4.190A pdb=" N ARG T 111 " --> pdb=" O ASP T 102 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU T 122 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU T 41 " --> pdb=" O LEU T 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU T 31 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL T 12 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE T 60 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU T 7 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU T 58 " --> pdb=" O GLU T 7 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE T 9 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE T 56 " --> pdb=" O ILE T 9 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL T 96 " --> pdb=" O SER T 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER T 117 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG T 98 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 26 through 28 Processing sheet with id=AI5, first strand: chain 'U' and resid 80 through 81 Processing sheet with id=AI6, first strand: chain 'W' and resid 21 through 23 2252 hydrogen bonds defined for protein. 6324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.43 Time building geometry restraints manager: 13.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 18152 1.35 - 1.46: 11824 1.46 - 1.58: 24880 1.58 - 1.70: 0 1.70 - 1.82: 496 Bond restraints: 55352 Sorted by residual: bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 55347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 73182 1.02 - 2.04: 1199 2.04 - 3.07: 189 3.07 - 4.09: 211 4.09 - 5.11: 5 Bond angle restraints: 74786 Sorted by residual: angle pdb=" C ASN B 227 " pdb=" CA ASN B 227 " pdb=" CB ASN B 227 " ideal model delta sigma weight residual 110.42 114.55 -4.13 1.99e+00 2.53e-01 4.31e+00 angle pdb=" C ASN N 227 " pdb=" CA ASN N 227 " pdb=" CB ASN N 227 " ideal model delta sigma weight residual 110.42 114.55 -4.13 1.99e+00 2.53e-01 4.30e+00 angle pdb=" CA LYS F 50 " pdb=" CB LYS F 50 " pdb=" CG LYS F 50 " ideal model delta sigma weight residual 114.10 117.63 -3.53 2.00e+00 2.50e-01 3.11e+00 angle pdb=" CA LYS R 50 " pdb=" CB LYS R 50 " pdb=" CG LYS R 50 " ideal model delta sigma weight residual 114.10 117.57 -3.47 2.00e+00 2.50e-01 3.01e+00 angle pdb=" CA GLY M1483 " pdb=" C GLY M1483 " pdb=" N MET M1484 " ideal model delta sigma weight residual 115.34 116.74 -1.40 8.10e-01 1.52e+00 2.97e+00 ... (remaining 74781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 30793 17.90 - 35.79: 2505 35.79 - 53.69: 450 53.69 - 71.59: 98 71.59 - 89.49: 74 Dihedral angle restraints: 33920 sinusoidal: 14154 harmonic: 19766 Sorted by residual: dihedral pdb=" CA GLU B 226 " pdb=" C GLU B 226 " pdb=" N ASN B 227 " pdb=" CA ASN B 227 " ideal model delta harmonic sigma weight residual -180.00 -134.77 -45.23 0 5.00e+00 4.00e-02 8.18e+01 dihedral pdb=" CA GLU N 226 " pdb=" C GLU N 226 " pdb=" N ASN N 227 " pdb=" CA ASN N 227 " ideal model delta harmonic sigma weight residual -180.00 -134.79 -45.21 0 5.00e+00 4.00e-02 8.18e+01 dihedral pdb=" CA CYS O 90 " pdb=" C CYS O 90 " pdb=" N GLU O 91 " pdb=" CA GLU O 91 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 33917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5836 0.030 - 0.060: 1511 0.060 - 0.090: 442 0.090 - 0.120: 523 0.120 - 0.150: 50 Chirality restraints: 8362 Sorted by residual: chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE M 596 " pdb=" N ILE M 596 " pdb=" C ILE M 596 " pdb=" CB ILE M 596 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE V 3 " pdb=" N ILE V 3 " pdb=" C ILE V 3 " pdb=" CB ILE V 3 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 8359 not shown) Planarity restraints: 9702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 395 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO M 396 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO M 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 395 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 396 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN S 122 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" CG ASN S 122 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN S 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN S 122 " -0.010 2.00e-02 2.50e+03 ... (remaining 9699 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 426 2.55 - 3.14: 44606 3.14 - 3.73: 86096 3.73 - 4.31: 120717 4.31 - 4.90: 201585 Nonbonded interactions: 453430 Sorted by model distance: nonbonded pdb=" OG SER M 867 " pdb=" OG1 THR M1415 " model vdw 1.969 3.040 nonbonded pdb=" OG SER A 867 " pdb=" OG1 THR A1415 " model vdw 1.969 3.040 nonbonded pdb=" OD1 ASN M 372 " pdb=" OH TYR N 788 " model vdw 1.985 3.040 nonbonded pdb=" OD1 ASN A 372 " pdb=" OH TYR B 788 " model vdw 1.987 3.040 nonbonded pdb=" OH TYR M 763 " pdb=" OD2 ASP T 23 " model vdw 2.012 3.040 ... (remaining 453425 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' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.930 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 135.600 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 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 : 0.002 0.033 55352 Z= 0.112 Angle : 0.386 5.112 74786 Z= 0.211 Chirality : 0.039 0.150 8362 Planarity : 0.002 0.058 9702 Dihedral : 14.045 89.486 21124 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 6690 helix: 2.04 (0.12), residues: 2172 sheet: 0.21 (0.16), residues: 992 loop : 0.33 (0.11), residues: 3526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 586 HIS 0.003 0.000 HIS C 60 PHE 0.007 0.000 PHE A 397 TYR 0.018 0.001 TYR L 41 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1823 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1823 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ASN cc_start: 0.5073 (p0) cc_final: 0.4572 (p0) REVERT: A 1086 MET cc_start: 0.7114 (mmt) cc_final: 0.6876 (mmm) REVERT: A 1158 LEU cc_start: 0.7586 (tt) cc_final: 0.6951 (tt) REVERT: A 1471 PHE cc_start: 0.7860 (p90) cc_final: 0.7604 (p90) REVERT: B 204 THR cc_start: 0.8148 (p) cc_final: 0.7034 (m) REVERT: B 412 LEU cc_start: 0.6955 (mt) cc_final: 0.6668 (pp) REVERT: B 452 ASN cc_start: 0.5771 (m-40) cc_final: 0.5510 (m-40) REVERT: B 504 THR cc_start: 0.8342 (p) cc_final: 0.8088 (m) REVERT: B 548 TRP cc_start: 0.7209 (m100) cc_final: 0.6568 (t-100) REVERT: B 848 LEU cc_start: 0.7802 (mt) cc_final: 0.7457 (mp) REVERT: B 956 PHE cc_start: 0.7061 (p90) cc_final: 0.6529 (p90) REVERT: G 46 ILE cc_start: 0.7166 (pt) cc_final: 0.6896 (pt) REVERT: G 97 LEU cc_start: 0.7094 (mt) cc_final: 0.6885 (mp) REVERT: H 79 ASP cc_start: 0.6308 (m-30) cc_final: 0.5947 (p0) REVERT: I 14 ILE cc_start: 0.8012 (mt) cc_final: 0.6848 (mt) REVERT: I 58 ILE cc_start: 0.8127 (mp) cc_final: 0.7874 (mm) REVERT: I 75 ASP cc_start: 0.6689 (t0) cc_final: 0.6206 (t0) REVERT: I 77 THR cc_start: 0.8640 (p) cc_final: 0.8322 (p) REVERT: K 24 ASP cc_start: 0.6659 (t70) cc_final: 0.6280 (t0) REVERT: M 502 ASN cc_start: 0.5206 (p0) cc_final: 0.4518 (p0) REVERT: M 629 VAL cc_start: 0.8780 (t) cc_final: 0.8512 (t) REVERT: M 1158 LEU cc_start: 0.7946 (tt) cc_final: 0.7100 (tt) REVERT: N 204 THR cc_start: 0.8146 (p) cc_final: 0.7132 (m) REVERT: N 260 LEU cc_start: 0.8061 (mm) cc_final: 0.7803 (mt) REVERT: N 412 LEU cc_start: 0.6641 (mt) cc_final: 0.6397 (pp) REVERT: N 548 TRP cc_start: 0.6976 (m100) cc_final: 0.6693 (t-100) REVERT: N 550 MET cc_start: 0.7570 (tmm) cc_final: 0.7352 (tpp) REVERT: N 584 MET cc_start: 0.7106 (mmm) cc_final: 0.6874 (mmm) REVERT: N 848 LEU cc_start: 0.7890 (mt) cc_final: 0.7556 (mp) REVERT: N 956 PHE cc_start: 0.7469 (p90) cc_final: 0.6753 (p90) REVERT: S 46 ILE cc_start: 0.7094 (pt) cc_final: 0.6858 (pt) REVERT: S 97 LEU cc_start: 0.7097 (mt) cc_final: 0.6630 (mp) REVERT: S 109 SER cc_start: 0.8249 (p) cc_final: 0.7882 (m) REVERT: U 14 ILE cc_start: 0.8065 (mt) cc_final: 0.7081 (mt) REVERT: U 34 ILE cc_start: 0.7863 (tp) cc_final: 0.7102 (mm) REVERT: U 75 ASP cc_start: 0.6649 (t0) cc_final: 0.6248 (t0) REVERT: U 77 THR cc_start: 0.8632 (p) cc_final: 0.8397 (p) REVERT: W 111 ASP cc_start: 0.7471 (m-30) cc_final: 0.7243 (m-30) outliers start: 0 outliers final: 0 residues processed: 1823 average time/residue: 0.5996 time to fit residues: 1794.3300 Evaluate side-chains 868 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 868 time to evaluate : 4.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 3.9990 chunk 503 optimal weight: 0.0070 chunk 279 optimal weight: 9.9990 chunk 171 optimal weight: 0.0970 chunk 339 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 520 optimal weight: 5.9990 chunk 201 optimal weight: 0.0770 chunk 316 optimal weight: 5.9990 chunk 387 optimal weight: 10.0000 chunk 602 optimal weight: 0.4980 overall best weight: 0.9356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN ** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 111 ASN B 525 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN C 32 ASN D 48 ASN D 55 GLN D 66 ASN E 65 ASN G 91 GLN G 93 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN K 40 HIS ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1082 HIS M1194 ASN M1410 HIS ** N 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 ASN ** N 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 ASN P 66 ASN Q 65 ASN S 91 GLN S 93 ASN ** S 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS ** U 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 55352 Z= 0.244 Angle : 0.657 11.090 74786 Z= 0.342 Chirality : 0.046 0.329 8362 Planarity : 0.005 0.070 9702 Dihedral : 3.617 45.170 7396 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.44 % Allowed : 12.28 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.59 (0.10), residues: 6690 helix: 1.15 (0.11), residues: 2306 sheet: 0.01 (0.16), residues: 1018 loop : 0.11 (0.11), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 27 HIS 0.014 0.001 HIS A 620 PHE 0.029 0.002 PHE K 13 TYR 0.022 0.002 TYR V 43 ARG 0.010 0.001 ARG B 924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 962 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.6819 (ptt) cc_final: 0.6544 (ptt) REVERT: A 1077 ASN cc_start: 0.8046 (m-40) cc_final: 0.7750 (m110) REVERT: B 548 TRP cc_start: 0.7151 (m100) cc_final: 0.6456 (t-100) REVERT: B 674 MET cc_start: 0.7874 (tpp) cc_final: 0.7556 (tpp) REVERT: B 733 MET cc_start: 0.7922 (ppp) cc_final: 0.7418 (ptm) REVERT: B 848 LEU cc_start: 0.7703 (mt) cc_final: 0.7392 (mp) REVERT: E 72 MET cc_start: 0.4658 (mmm) cc_final: 0.4248 (mmm) REVERT: J 12 LYS cc_start: 0.7727 (tptt) cc_final: 0.7520 (tptm) REVERT: M 982 ASN cc_start: 0.6644 (t0) cc_final: 0.6328 (t0) REVERT: M 1077 ASN cc_start: 0.7965 (m-40) cc_final: 0.7674 (m110) REVERT: M 1086 MET cc_start: 0.7024 (mmm) cc_final: 0.6811 (mmm) REVERT: M 1166 LEU cc_start: 0.8285 (tt) cc_final: 0.7789 (tt) REVERT: M 1484 MET cc_start: 0.6444 (pmm) cc_final: 0.6143 (pmm) REVERT: N 548 TRP cc_start: 0.6812 (m100) cc_final: 0.6571 (t-100) REVERT: N 728 MET cc_start: 0.6663 (mmt) cc_final: 0.6229 (tpp) REVERT: N 731 GLN cc_start: 0.7849 (mt0) cc_final: 0.7430 (mt0) REVERT: N 848 LEU cc_start: 0.7781 (mt) cc_final: 0.7441 (mp) REVERT: O 41 GLU cc_start: 0.5244 (tm-30) cc_final: 0.5034 (tm-30) REVERT: O 101 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: O 244 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6901 (mm) REVERT: R 80 MET cc_start: 0.5942 (mpp) cc_final: 0.5238 (mmm) REVERT: W 19 ILE cc_start: 0.8494 (tp) cc_final: 0.8241 (tt) outliers start: 147 outliers final: 81 residues processed: 1061 average time/residue: 0.5594 time to fit residues: 1012.8834 Evaluate side-chains 805 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 722 time to evaluate : 5.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 49 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 636 ILE Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1358 THR Chi-restraints excluded: chain M residue 1412 MET Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 590 LEU Chi-restraints excluded: chain N residue 667 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 760 THR Chi-restraints excluded: chain N residue 897 ARG Chi-restraints excluded: chain N residue 1043 ILE Chi-restraints excluded: chain O residue 101 PHE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 15 ILE Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 117 SER Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 72 ILE Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 501 optimal weight: 0.2980 chunk 410 optimal weight: 0.1980 chunk 166 optimal weight: 6.9990 chunk 604 optimal weight: 8.9990 chunk 652 optimal weight: 7.9990 chunk 537 optimal weight: 0.2980 chunk 599 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 484 optimal weight: 1.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1263 ASN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** M 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1194 ASN ** M1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 197 GLN ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 941 GLN P 93 HIS U 91 HIS ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55352 Z= 0.188 Angle : 0.596 9.862 74786 Z= 0.305 Chirality : 0.045 0.287 8362 Planarity : 0.004 0.073 9702 Dihedral : 3.752 44.454 7396 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.79 % Allowed : 14.61 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.44 (0.10), residues: 6690 helix: 1.05 (0.11), residues: 2328 sheet: -0.04 (0.16), residues: 976 loop : -0.03 (0.11), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 27 HIS 0.020 0.001 HIS A 432 PHE 0.033 0.002 PHE K 13 TYR 0.021 0.001 TYR V 43 ARG 0.009 0.001 ARG R 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 833 time to evaluate : 6.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1130 ILE cc_start: 0.7730 (mm) cc_final: 0.7526 (mm) REVERT: B 276 LEU cc_start: 0.8061 (mm) cc_final: 0.7475 (mm) REVERT: B 504 THR cc_start: 0.8465 (p) cc_final: 0.8107 (t) REVERT: B 550 MET cc_start: 0.7013 (tpp) cc_final: 0.6458 (tpt) REVERT: B 573 TRP cc_start: 0.6485 (OUTLIER) cc_final: 0.5719 (t60) REVERT: B 674 MET cc_start: 0.7869 (tpp) cc_final: 0.7444 (tpp) REVERT: B 733 MET cc_start: 0.7807 (ppp) cc_final: 0.7333 (ptm) REVERT: B 786 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8640 (t) REVERT: B 840 MET cc_start: 0.5669 (tmm) cc_final: 0.5303 (tmm) REVERT: B 848 LEU cc_start: 0.7725 (mt) cc_final: 0.7418 (mp) REVERT: G 140 ASP cc_start: 0.7489 (m-30) cc_final: 0.7178 (t70) REVERT: H 98 ARG cc_start: 0.7321 (ttm110) cc_final: 0.7056 (ttm110) REVERT: I 18 GLN cc_start: 0.8268 (mp10) cc_final: 0.8058 (mm110) REVERT: I 73 SER cc_start: 0.8696 (p) cc_final: 0.8484 (t) REVERT: K 1 MET cc_start: 0.6137 (ttm) cc_final: 0.5772 (ttm) REVERT: K 112 LYS cc_start: 0.8466 (mmmm) cc_final: 0.7878 (mmmm) REVERT: M 561 MET cc_start: 0.7392 (mmt) cc_final: 0.7186 (mmt) REVERT: M 565 MET cc_start: 0.7071 (tpp) cc_final: 0.6832 (tpp) REVERT: M 1077 ASN cc_start: 0.7850 (m-40) cc_final: 0.6807 (m-40) REVERT: M 1130 ILE cc_start: 0.7517 (mm) cc_final: 0.7307 (mm) REVERT: N 548 TRP cc_start: 0.6782 (m100) cc_final: 0.6410 (t-100) REVERT: N 573 TRP cc_start: 0.6138 (OUTLIER) cc_final: 0.5228 (t60) REVERT: N 577 HIS cc_start: 0.6718 (t-90) cc_final: 0.6417 (t-90) REVERT: N 674 MET cc_start: 0.8000 (tpp) cc_final: 0.7121 (mtp) REVERT: N 728 MET cc_start: 0.6560 (mmt) cc_final: 0.6190 (tpp) REVERT: N 848 LEU cc_start: 0.7820 (mt) cc_final: 0.7485 (mp) REVERT: N 954 MET cc_start: 0.7461 (mmm) cc_final: 0.7131 (mmm) REVERT: O 244 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6943 (mm) REVERT: P 111 SER cc_start: 0.8766 (p) cc_final: 0.8530 (m) REVERT: R 80 MET cc_start: 0.5471 (mpp) cc_final: 0.5101 (mmm) REVERT: R 90 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8317 (mt) REVERT: S 100 GLU cc_start: 0.6165 (tt0) cc_final: 0.5742 (tm-30) REVERT: U 112 TYR cc_start: 0.8120 (m-80) cc_final: 0.7894 (m-80) REVERT: V 12 LYS cc_start: 0.7837 (tptt) cc_final: 0.7562 (tptm) REVERT: X 44 MET cc_start: 0.6236 (tpp) cc_final: 0.5504 (mmp) outliers start: 168 outliers final: 99 residues processed: 945 average time/residue: 0.5407 time to fit residues: 873.3414 Evaluate side-chains 787 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 683 time to evaluate : 5.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 49 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 636 ILE Chi-restraints excluded: chain M residue 812 LYS Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 908 THR Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 1060 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1412 MET Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 358 GLU Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 590 LEU Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 0.8980 chunk 454 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 288 optimal weight: 0.5980 chunk 405 optimal weight: 4.9990 chunk 606 optimal weight: 4.9990 chunk 641 optimal weight: 10.0000 chunk 316 optimal weight: 0.8980 chunk 574 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN B 344 GLN ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 43 HIS E 132 GLN I 67 GLN I 91 HIS ** M 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 780 ASN ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1005 HIS M1182 GLN M1194 ASN M1299 GLN N 144 HIS N 344 GLN ** N 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS U 91 HIS ** V 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 55352 Z= 0.309 Angle : 0.639 12.292 74786 Z= 0.327 Chirality : 0.046 0.302 8362 Planarity : 0.005 0.074 9702 Dihedral : 4.040 43.741 7396 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.00 % Allowed : 16.14 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.36 (0.10), residues: 6690 helix: 0.95 (0.11), residues: 2332 sheet: -0.09 (0.16), residues: 968 loop : -0.05 (0.11), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 27 HIS 0.016 0.001 HIS A 432 PHE 0.032 0.002 PHE K 13 TYR 0.025 0.002 TYR B 752 ARG 0.008 0.001 ARG M 954 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 737 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1292 MET cc_start: 0.8237 (ppp) cc_final: 0.7601 (ppp) REVERT: A 1293 LEU cc_start: 0.7380 (tp) cc_final: 0.7103 (tp) REVERT: B 45 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6674 (t70) REVERT: B 222 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7078 (ptt180) REVERT: B 504 THR cc_start: 0.8576 (p) cc_final: 0.8373 (p) REVERT: B 508 MET cc_start: 0.7002 (mtt) cc_final: 0.6793 (mtt) REVERT: B 531 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7017 (p90) REVERT: B 573 TRP cc_start: 0.6840 (OUTLIER) cc_final: 0.5468 (t60) REVERT: B 674 MET cc_start: 0.8024 (tpp) cc_final: 0.7772 (tpp) REVERT: B 733 MET cc_start: 0.8036 (ppp) cc_final: 0.7635 (ptm) REVERT: B 840 MET cc_start: 0.5887 (tmm) cc_final: 0.5476 (tmm) REVERT: B 848 LEU cc_start: 0.7876 (mt) cc_final: 0.7582 (mt) REVERT: C 101 PHE cc_start: 0.7664 (m-80) cc_final: 0.7376 (m-80) REVERT: F 94 MET cc_start: 0.8086 (tpt) cc_final: 0.7846 (tpt) REVERT: G 100 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: H 98 ARG cc_start: 0.7417 (ttm110) cc_final: 0.7192 (ttm110) REVERT: I 108 MET cc_start: 0.7719 (tpp) cc_final: 0.7403 (mmp) REVERT: K 1 MET cc_start: 0.6279 (ttm) cc_final: 0.6062 (ttm) REVERT: K 70 LYS cc_start: 0.8256 (ptmt) cc_final: 0.7938 (ptpp) REVERT: L 44 MET cc_start: 0.6212 (tpp) cc_final: 0.5852 (mmp) REVERT: M 565 MET cc_start: 0.7655 (tpp) cc_final: 0.7269 (tpp) REVERT: M 1130 ILE cc_start: 0.7792 (mm) cc_final: 0.7471 (mm) REVERT: M 1293 LEU cc_start: 0.7657 (tp) cc_final: 0.7110 (tp) REVERT: N 548 TRP cc_start: 0.7305 (m100) cc_final: 0.6837 (t-100) REVERT: N 573 TRP cc_start: 0.6650 (OUTLIER) cc_final: 0.5156 (t60) REVERT: N 674 MET cc_start: 0.8093 (tpp) cc_final: 0.7468 (mtp) REVERT: N 728 MET cc_start: 0.7160 (mmt) cc_final: 0.6829 (tpp) REVERT: N 848 LEU cc_start: 0.7897 (mt) cc_final: 0.7558 (mp) REVERT: N 1000 THR cc_start: 0.8515 (m) cc_final: 0.8210 (p) REVERT: Q 103 LEU cc_start: 0.8315 (pp) cc_final: 0.7947 (pt) REVERT: R 80 MET cc_start: 0.5867 (mpp) cc_final: 0.5259 (mmm) REVERT: U 73 SER cc_start: 0.8813 (p) cc_final: 0.8578 (t) REVERT: V 12 LYS cc_start: 0.8023 (tptt) cc_final: 0.7680 (tptp) REVERT: X 44 MET cc_start: 0.6202 (mpp) cc_final: 0.5536 (mmt) outliers start: 241 outliers final: 148 residues processed: 911 average time/residue: 0.5203 time to fit residues: 817.4355 Evaluate side-chains 794 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 640 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 796 LYS Chi-restraints excluded: chain M residue 812 LYS Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 889 LEU Chi-restraints excluded: chain M residue 908 THR Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 968 VAL Chi-restraints excluded: chain M residue 1045 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1358 THR Chi-restraints excluded: chain M residue 1367 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 144 HIS Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 358 GLU Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 590 LEU Chi-restraints excluded: chain N residue 598 VAL Chi-restraints excluded: chain N residue 667 THR Chi-restraints excluded: chain N residue 692 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 760 THR Chi-restraints excluded: chain N residue 933 ASP Chi-restraints excluded: chain N residue 1043 ILE Chi-restraints excluded: chain N residue 1055 VAL Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 22 HIS Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 67 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 1.9990 chunk 364 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 477 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 547 optimal weight: 1.9990 chunk 443 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 327 optimal weight: 4.9990 chunk 576 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 525 ASN B 639 HIS ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS E 132 GLN ** M 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 485 ASN ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 639 HIS ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 986 GLN O 265 HIS U 67 GLN U 91 HIS V 52 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 55352 Z= 0.302 Angle : 0.622 12.367 74786 Z= 0.317 Chirality : 0.045 0.324 8362 Planarity : 0.004 0.070 9702 Dihedral : 4.158 41.974 7396 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.82 % Allowed : 17.76 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 6690 helix: 0.93 (0.11), residues: 2326 sheet: -0.23 (0.16), residues: 880 loop : -0.11 (0.10), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 27 HIS 0.028 0.002 HIS N 144 PHE 0.035 0.002 PHE K 13 TYR 0.023 0.002 TYR B 752 ARG 0.010 0.001 ARG S 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 705 time to evaluate : 4.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.4267 (tmm) cc_final: 0.3866 (ttp) REVERT: A 1292 MET cc_start: 0.8113 (ppp) cc_final: 0.7578 (ppp) REVERT: A 1293 LEU cc_start: 0.7524 (tp) cc_final: 0.7235 (tp) REVERT: B 45 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6625 (t70) REVERT: B 347 MET cc_start: 0.7497 (ttp) cc_final: 0.7154 (ttm) REVERT: B 504 THR cc_start: 0.8566 (p) cc_final: 0.8219 (t) REVERT: B 531 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7146 (p90) REVERT: B 553 LEU cc_start: 0.6481 (mt) cc_final: 0.4403 (mt) REVERT: B 573 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.5649 (t60) REVERT: B 611 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6624 (mt-10) REVERT: B 674 MET cc_start: 0.8144 (tpp) cc_final: 0.7738 (tpp) REVERT: B 733 MET cc_start: 0.8010 (ppp) cc_final: 0.7696 (ptm) REVERT: B 840 MET cc_start: 0.5889 (tmm) cc_final: 0.5553 (tmm) REVERT: B 848 LEU cc_start: 0.7877 (mt) cc_final: 0.7591 (mt) REVERT: B 983 GLU cc_start: 0.6421 (tt0) cc_final: 0.5967 (pt0) REVERT: B 1000 THR cc_start: 0.8518 (m) cc_final: 0.8237 (p) REVERT: C 101 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: D 128 GLN cc_start: 0.7736 (tp40) cc_final: 0.7332 (pt0) REVERT: I 108 MET cc_start: 0.7858 (tpp) cc_final: 0.7518 (mmp) REVERT: K 70 LYS cc_start: 0.8339 (ptmt) cc_final: 0.8005 (ptpp) REVERT: K 112 LYS cc_start: 0.8581 (mmmm) cc_final: 0.7957 (mmmm) REVERT: M 1015 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7065 (tm-30) REVERT: M 1130 ILE cc_start: 0.8199 (mm) cc_final: 0.7989 (mm) REVERT: M 1231 ILE cc_start: 0.9006 (pt) cc_final: 0.8757 (mp) REVERT: M 1292 MET cc_start: 0.8315 (ppp) cc_final: 0.7192 (ppp) REVERT: M 1293 LEU cc_start: 0.7678 (tp) cc_final: 0.6996 (tp) REVERT: M 1296 MET cc_start: 0.7723 (mtp) cc_final: 0.7420 (mtp) REVERT: N 531 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6886 (p90) REVERT: N 573 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.5034 (t60) REVERT: N 674 MET cc_start: 0.8204 (tpp) cc_final: 0.7573 (mtp) REVERT: N 728 MET cc_start: 0.7487 (mmt) cc_final: 0.7143 (tpp) REVERT: N 769 PHE cc_start: 0.8404 (t80) cc_final: 0.7942 (t80) REVERT: N 840 MET cc_start: 0.6263 (tmm) cc_final: 0.6003 (tmm) REVERT: N 848 LEU cc_start: 0.7966 (mt) cc_final: 0.7623 (mp) REVERT: N 954 MET cc_start: 0.7685 (mmm) cc_final: 0.7473 (mmm) REVERT: N 956 PHE cc_start: 0.8308 (p90) cc_final: 0.7911 (p90) REVERT: O 101 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: U 73 SER cc_start: 0.8865 (p) cc_final: 0.8657 (t) REVERT: V 12 LYS cc_start: 0.7953 (tptt) cc_final: 0.7683 (tptp) REVERT: X 43 ILE cc_start: 0.6957 (mt) cc_final: 0.6631 (mt) REVERT: X 44 MET cc_start: 0.6080 (mpp) cc_final: 0.5405 (mmt) outliers start: 230 outliers final: 168 residues processed: 869 average time/residue: 0.5102 time to fit residues: 767.3870 Evaluate side-chains 809 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 634 time to evaluate : 4.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 564 LEU Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 636 ILE Chi-restraints excluded: chain M residue 713 VAL Chi-restraints excluded: chain M residue 796 LYS Chi-restraints excluded: chain M residue 812 LYS Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 908 THR Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 968 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1045 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1358 THR Chi-restraints excluded: chain M residue 1367 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 358 GLU Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 526 LEU Chi-restraints excluded: chain N residue 531 TYR Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 667 THR Chi-restraints excluded: chain N residue 692 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 866 ILE Chi-restraints excluded: chain N residue 870 THR Chi-restraints excluded: chain N residue 933 ASP Chi-restraints excluded: chain N residue 1043 ILE Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 101 PHE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 22 HIS Chi-restraints excluded: chain Q residue 40 PHE Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 215 optimal weight: 7.9990 chunk 577 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 376 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 642 optimal weight: 10.0000 chunk 533 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 212 optimal weight: 0.7980 chunk 337 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS B 144 HIS ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 265 HIS D 34 ASN D 102 ASN E 132 GLN ** M 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS ** N 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 254 GLN ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 930 GLN ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 260 GLN O 265 HIS Q 132 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 55352 Z= 0.197 Angle : 0.587 14.676 74786 Z= 0.295 Chirality : 0.045 0.332 8362 Planarity : 0.004 0.070 9702 Dihedral : 4.079 43.650 7396 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.50 % Allowed : 18.66 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.36 (0.10), residues: 6690 helix: 1.06 (0.11), residues: 2316 sheet: -0.13 (0.16), residues: 920 loop : -0.12 (0.11), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 27 HIS 0.023 0.001 HIS B 144 PHE 0.035 0.001 PHE S 18 TYR 0.016 0.001 TYR B 531 ARG 0.009 0.000 ARG S 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 717 time to evaluate : 5.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.4328 (tmm) cc_final: 0.3802 (ttp) REVERT: A 1292 MET cc_start: 0.8025 (ppp) cc_final: 0.7582 (ppp) REVERT: A 1293 LEU cc_start: 0.7420 (tp) cc_final: 0.7120 (tp) REVERT: B 27 TRP cc_start: 0.7228 (m100) cc_final: 0.6907 (m100) REVERT: B 45 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6572 (t70) REVERT: B 200 MET cc_start: 0.7720 (mmm) cc_final: 0.7130 (mmt) REVERT: B 222 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6908 (ptt180) REVERT: B 347 MET cc_start: 0.7473 (ttp) cc_final: 0.7129 (ttm) REVERT: B 470 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8268 (tp) REVERT: B 504 THR cc_start: 0.8484 (p) cc_final: 0.8270 (t) REVERT: B 531 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7081 (p90) REVERT: B 553 LEU cc_start: 0.6353 (mt) cc_final: 0.4376 (mt) REVERT: B 573 TRP cc_start: 0.6871 (OUTLIER) cc_final: 0.5506 (t60) REVERT: B 611 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6642 (mt-10) REVERT: B 733 MET cc_start: 0.7948 (ppp) cc_final: 0.7498 (ptm) REVERT: B 840 MET cc_start: 0.5833 (tmm) cc_final: 0.5489 (tmm) REVERT: B 848 LEU cc_start: 0.7881 (mt) cc_final: 0.7608 (mp) REVERT: B 954 MET cc_start: 0.7238 (mmm) cc_final: 0.6990 (mmm) REVERT: B 983 GLU cc_start: 0.6320 (tt0) cc_final: 0.5930 (pt0) REVERT: C 131 THR cc_start: 0.6868 (OUTLIER) cc_final: 0.6632 (p) REVERT: D 36 GLU cc_start: 0.7302 (tp30) cc_final: 0.7018 (tp30) REVERT: D 128 GLN cc_start: 0.7707 (tp40) cc_final: 0.7378 (pt0) REVERT: I 108 MET cc_start: 0.7827 (tpp) cc_final: 0.7547 (mmp) REVERT: J 58 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7603 (ttmm) REVERT: K 41 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7863 (t) REVERT: K 112 LYS cc_start: 0.8457 (mmmm) cc_final: 0.7999 (mmmm) REVERT: M 565 MET cc_start: 0.7684 (tpp) cc_final: 0.7018 (tpp) REVERT: M 1130 ILE cc_start: 0.8057 (mm) cc_final: 0.7779 (mm) REVERT: M 1234 LYS cc_start: 0.8133 (tmtt) cc_final: 0.7859 (tttt) REVERT: M 1292 MET cc_start: 0.8240 (ppp) cc_final: 0.7560 (ppp) REVERT: M 1293 LEU cc_start: 0.7655 (tp) cc_final: 0.7093 (tp) REVERT: N 531 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6863 (p90) REVERT: N 573 TRP cc_start: 0.6678 (OUTLIER) cc_final: 0.4874 (t60) REVERT: N 674 MET cc_start: 0.8111 (tpp) cc_final: 0.7405 (mtp) REVERT: N 769 PHE cc_start: 0.8353 (t80) cc_final: 0.7969 (t80) REVERT: N 840 MET cc_start: 0.6165 (tmm) cc_final: 0.5937 (tmm) REVERT: N 848 LEU cc_start: 0.7900 (mt) cc_final: 0.7577 (mp) REVERT: O 101 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: S 110 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7542 (tpp80) REVERT: T 13 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7951 (tmtt) REVERT: U 73 SER cc_start: 0.8805 (p) cc_final: 0.8590 (t) REVERT: V 12 LYS cc_start: 0.7821 (tptt) cc_final: 0.7620 (tptp) REVERT: X 43 ILE cc_start: 0.6888 (mt) cc_final: 0.6601 (mt) REVERT: X 44 MET cc_start: 0.6103 (mpp) cc_final: 0.5519 (mmt) outliers start: 211 outliers final: 146 residues processed: 865 average time/residue: 0.5207 time to fit residues: 776.1403 Evaluate side-chains 784 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 627 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 713 VAL Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1163 HIS Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1309 MET Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 358 GLU Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 526 LEU Chi-restraints excluded: chain N residue 531 TYR Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 596 ILE Chi-restraints excluded: chain N residue 598 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 667 THR Chi-restraints excluded: chain N residue 692 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 752 TYR Chi-restraints excluded: chain N residue 866 ILE Chi-restraints excluded: chain N residue 870 THR Chi-restraints excluded: chain N residue 933 ASP Chi-restraints excluded: chain N residue 1043 ILE Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 101 PHE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain Q residue 22 HIS Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 13 LYS Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 619 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 366 optimal weight: 0.6980 chunk 469 optimal weight: 6.9990 chunk 363 optimal weight: 2.9990 chunk 540 optimal weight: 0.7980 chunk 358 optimal weight: 4.9990 chunk 639 optimal weight: 0.5980 chunk 400 optimal weight: 1.9990 chunk 390 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 315 ASN ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 34 ASN E 132 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 504 HIS M 678 ASN ** M 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1042 ASN M1263 ASN N 144 HIS ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 55352 Z= 0.196 Angle : 0.601 17.579 74786 Z= 0.300 Chirality : 0.044 0.308 8362 Planarity : 0.004 0.070 9702 Dihedral : 4.054 42.675 7396 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.44 % Allowed : 19.16 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.10), residues: 6690 helix: 1.06 (0.11), residues: 2316 sheet: -0.15 (0.16), residues: 952 loop : -0.13 (0.11), residues: 3422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 27 HIS 0.020 0.001 HIS B 144 PHE 0.024 0.002 PHE S 18 TYR 0.047 0.001 TYR L 41 ARG 0.009 0.000 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 675 time to evaluate : 4.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.4343 (tmm) cc_final: 0.3613 (ttp) REVERT: A 1292 MET cc_start: 0.8063 (ppp) cc_final: 0.7496 (ppp) REVERT: A 1293 LEU cc_start: 0.7365 (tp) cc_final: 0.7147 (tp) REVERT: B 45 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6528 (t70) REVERT: B 200 MET cc_start: 0.7730 (mmm) cc_final: 0.7189 (mmt) REVERT: B 222 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6878 (ptt180) REVERT: B 276 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 347 MET cc_start: 0.7511 (ttp) cc_final: 0.7113 (ttm) REVERT: B 470 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8276 (tp) REVERT: B 504 THR cc_start: 0.8516 (p) cc_final: 0.8262 (t) REVERT: B 531 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7075 (p90) REVERT: B 553 LEU cc_start: 0.6300 (mt) cc_final: 0.3712 (mt) REVERT: B 573 TRP cc_start: 0.6885 (OUTLIER) cc_final: 0.5284 (t60) REVERT: B 611 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6675 (mt-10) REVERT: B 733 MET cc_start: 0.7884 (ppp) cc_final: 0.7482 (ptm) REVERT: B 840 MET cc_start: 0.5789 (tmm) cc_final: 0.5459 (tmm) REVERT: B 848 LEU cc_start: 0.7940 (mt) cc_final: 0.7645 (mp) REVERT: B 954 MET cc_start: 0.7232 (mmm) cc_final: 0.6997 (mmm) REVERT: B 983 GLU cc_start: 0.6349 (tt0) cc_final: 0.5915 (pt0) REVERT: C 131 THR cc_start: 0.6959 (p) cc_final: 0.6736 (p) REVERT: D 36 GLU cc_start: 0.7286 (tp30) cc_final: 0.7080 (tp30) REVERT: D 128 GLN cc_start: 0.7662 (tp40) cc_final: 0.7372 (pt0) REVERT: G 139 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7872 (tm-30) REVERT: I 108 MET cc_start: 0.7827 (tpp) cc_final: 0.7531 (mmp) REVERT: K 41 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7942 (t) REVERT: K 112 LYS cc_start: 0.8329 (mmmm) cc_final: 0.7961 (mmmm) REVERT: M 565 MET cc_start: 0.7588 (tpp) cc_final: 0.7194 (tpp) REVERT: M 1130 ILE cc_start: 0.7965 (mm) cc_final: 0.7669 (mm) REVERT: M 1234 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7896 (tttt) REVERT: M 1292 MET cc_start: 0.8259 (ppp) cc_final: 0.8046 (ppp) REVERT: M 1293 LEU cc_start: 0.7661 (tp) cc_final: 0.7192 (tp) REVERT: M 1296 MET cc_start: 0.7580 (mtp) cc_final: 0.7267 (mtp) REVERT: N 531 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6892 (p90) REVERT: N 573 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.4994 (t60) REVERT: N 674 MET cc_start: 0.8083 (tpp) cc_final: 0.7438 (mtp) REVERT: N 769 PHE cc_start: 0.8342 (t80) cc_final: 0.8032 (t80) REVERT: N 840 MET cc_start: 0.6089 (tmm) cc_final: 0.5865 (tmm) REVERT: N 848 LEU cc_start: 0.7946 (mt) cc_final: 0.7624 (mp) REVERT: O 101 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: S 110 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7541 (tpp80) REVERT: S 140 ASP cc_start: 0.7966 (t0) cc_final: 0.7757 (t70) REVERT: U 73 SER cc_start: 0.8814 (p) cc_final: 0.8563 (t) REVERT: V 12 LYS cc_start: 0.7834 (tptt) cc_final: 0.7610 (tptp) REVERT: X 43 ILE cc_start: 0.6890 (mt) cc_final: 0.6608 (mt) REVERT: X 44 MET cc_start: 0.6076 (mpp) cc_final: 0.5481 (mmt) outliers start: 207 outliers final: 161 residues processed: 820 average time/residue: 0.5233 time to fit residues: 737.6262 Evaluate side-chains 802 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 631 time to evaluate : 4.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 481 THR Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 636 ILE Chi-restraints excluded: chain M residue 713 VAL Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1045 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1163 HIS Chi-restraints excluded: chain M residue 1166 LEU Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1309 MET Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 144 HIS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 358 GLU Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 526 LEU Chi-restraints excluded: chain N residue 531 TYR Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 596 ILE Chi-restraints excluded: chain N residue 598 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 692 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 752 TYR Chi-restraints excluded: chain N residue 866 ILE Chi-restraints excluded: chain N residue 870 THR Chi-restraints excluded: chain N residue 928 ILE Chi-restraints excluded: chain N residue 933 ASP Chi-restraints excluded: chain N residue 1043 ILE Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 101 PHE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 22 HIS Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 117 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 395 optimal weight: 0.0050 chunk 255 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 406 optimal weight: 9.9990 chunk 436 optimal weight: 0.9980 chunk 316 optimal weight: 0.0170 chunk 59 optimal weight: 0.4980 chunk 503 optimal weight: 0.4980 overall best weight: 0.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 913 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 HIS B 144 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS E 132 GLN F 72 GLN G 4 HIS ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 485 ASN M 721 HIS M 809 HIS ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 GLN N 500 GLN N 725 GLN ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55352 Z= 0.172 Angle : 0.610 15.633 74786 Z= 0.301 Chirality : 0.044 0.307 8362 Planarity : 0.004 0.071 9702 Dihedral : 3.994 41.687 7396 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.82 % Allowed : 19.94 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.40 (0.10), residues: 6690 helix: 1.13 (0.11), residues: 2314 sheet: -0.11 (0.16), residues: 904 loop : -0.14 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 236 HIS 0.013 0.001 HIS N 144 PHE 0.035 0.001 PHE N 956 TYR 0.041 0.001 TYR L 41 ARG 0.008 0.000 ARG N 938 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 680 time to evaluate : 5.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.4318 (tmm) cc_final: 0.3381 (ttp) REVERT: A 875 TYR cc_start: 0.7654 (m-80) cc_final: 0.7354 (m-80) REVERT: A 1292 MET cc_start: 0.8012 (ppp) cc_final: 0.7520 (ppp) REVERT: A 1293 LEU cc_start: 0.7279 (tp) cc_final: 0.6993 (tp) REVERT: B 119 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 200 MET cc_start: 0.7684 (mmm) cc_final: 0.7159 (mmt) REVERT: B 222 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6780 (ptt180) REVERT: B 276 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7244 (mm) REVERT: B 470 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (tp) REVERT: B 531 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7172 (p90) REVERT: B 553 LEU cc_start: 0.6233 (mt) cc_final: 0.3603 (mt) REVERT: B 573 TRP cc_start: 0.6803 (OUTLIER) cc_final: 0.5258 (t60) REVERT: B 611 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6625 (mt-10) REVERT: B 733 MET cc_start: 0.7813 (ppp) cc_final: 0.7402 (ptm) REVERT: B 840 MET cc_start: 0.5668 (tmm) cc_final: 0.5406 (tmm) REVERT: B 848 LEU cc_start: 0.7929 (mt) cc_final: 0.7638 (mp) REVERT: B 983 GLU cc_start: 0.6324 (tt0) cc_final: 0.5891 (pt0) REVERT: C 131 THR cc_start: 0.6940 (p) cc_final: 0.6702 (p) REVERT: D 36 GLU cc_start: 0.7264 (tp30) cc_final: 0.6983 (tp30) REVERT: D 128 GLN cc_start: 0.7609 (tp40) cc_final: 0.7385 (pt0) REVERT: F 61 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7645 (mt-10) REVERT: I 108 MET cc_start: 0.7836 (tpp) cc_final: 0.7613 (mmp) REVERT: K 41 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7855 (t) REVERT: K 112 LYS cc_start: 0.8203 (mmmm) cc_final: 0.7875 (mmmm) REVERT: M 520 MET cc_start: 0.6480 (mmp) cc_final: 0.6245 (mmm) REVERT: M 565 MET cc_start: 0.7638 (tpp) cc_final: 0.7316 (tpp) REVERT: M 587 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8313 (m) REVERT: M 1234 LYS cc_start: 0.8136 (tmtt) cc_final: 0.7861 (tttt) REVERT: M 1293 LEU cc_start: 0.7699 (tp) cc_final: 0.7294 (tp) REVERT: N 531 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6844 (p90) REVERT: N 573 TRP cc_start: 0.6837 (OUTLIER) cc_final: 0.4765 (t60) REVERT: N 674 MET cc_start: 0.8023 (tpp) cc_final: 0.7405 (mtp) REVERT: N 728 MET cc_start: 0.7221 (mmt) cc_final: 0.6893 (tpp) REVERT: N 769 PHE cc_start: 0.8289 (t80) cc_final: 0.8049 (t80) REVERT: N 848 LEU cc_start: 0.7964 (mt) cc_final: 0.7634 (mp) REVERT: O 101 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: R 90 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8191 (mt) REVERT: S 110 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7593 (tpp80) REVERT: S 140 ASP cc_start: 0.8023 (t0) cc_final: 0.7786 (t70) REVERT: T 92 MET cc_start: 0.6784 (ttm) cc_final: 0.6270 (ttm) REVERT: U 73 SER cc_start: 0.8753 (p) cc_final: 0.8474 (t) REVERT: V 12 LYS cc_start: 0.7754 (tptt) cc_final: 0.7497 (tptp) REVERT: X 43 ILE cc_start: 0.6833 (mt) cc_final: 0.6535 (mt) REVERT: X 44 MET cc_start: 0.6087 (mpp) cc_final: 0.5595 (mmt) outliers start: 170 outliers final: 117 residues processed: 800 average time/residue: 0.5075 time to fit residues: 700.4326 Evaluate side-chains 756 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 627 time to evaluate : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 587 THR Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 636 ILE Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1045 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1163 HIS Chi-restraints excluded: chain M residue 1284 PHE Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 526 LEU Chi-restraints excluded: chain N residue 531 TYR Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 596 ILE Chi-restraints excluded: chain N residue 598 VAL Chi-restraints excluded: chain N residue 692 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 752 TYR Chi-restraints excluded: chain N residue 928 ILE Chi-restraints excluded: chain N residue 933 ASP Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 101 PHE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 117 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 582 optimal weight: 5.9990 chunk 613 optimal weight: 6.9990 chunk 559 optimal weight: 10.0000 chunk 596 optimal weight: 6.9990 chunk 612 optimal weight: 5.9990 chunk 358 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 468 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 538 optimal weight: 0.9990 chunk 564 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 144 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 34 ASN D 102 ASN E 132 GLN F 72 GLN ** M 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN N 502 HIS ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS P 34 ASN P 102 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 55352 Z= 0.211 Angle : 0.624 15.844 74786 Z= 0.308 Chirality : 0.045 0.360 8362 Planarity : 0.004 0.070 9702 Dihedral : 4.027 41.550 7396 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.92 % Allowed : 20.09 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.41 (0.10), residues: 6690 helix: 1.16 (0.11), residues: 2318 sheet: -0.02 (0.16), residues: 902 loop : -0.17 (0.11), residues: 3470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 236 HIS 0.012 0.001 HIS C 265 PHE 0.031 0.001 PHE B 364 TYR 0.034 0.001 TYR L 41 ARG 0.014 0.000 ARG M 954 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 638 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.4423 (tmm) cc_final: 0.3464 (ttp) REVERT: A 962 ASP cc_start: 0.7603 (m-30) cc_final: 0.7360 (m-30) REVERT: A 1292 MET cc_start: 0.7993 (ppp) cc_final: 0.7623 (ppp) REVERT: A 1293 LEU cc_start: 0.7337 (tp) cc_final: 0.7040 (tp) REVERT: B 200 MET cc_start: 0.7737 (mmm) cc_final: 0.7138 (mmt) REVERT: B 222 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6769 (ptt180) REVERT: B 276 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7175 (mm) REVERT: B 388 TYR cc_start: 0.6729 (m-80) cc_final: 0.6408 (m-80) REVERT: B 531 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7124 (p90) REVERT: B 553 LEU cc_start: 0.6279 (mt) cc_final: 0.3636 (mt) REVERT: B 573 TRP cc_start: 0.6971 (OUTLIER) cc_final: 0.5387 (t60) REVERT: B 733 MET cc_start: 0.7872 (ppp) cc_final: 0.7509 (ptm) REVERT: B 802 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6946 (t0) REVERT: B 848 LEU cc_start: 0.8018 (mt) cc_final: 0.7784 (mt) REVERT: C 131 THR cc_start: 0.6971 (p) cc_final: 0.6720 (p) REVERT: D 128 GLN cc_start: 0.7642 (tp40) cc_final: 0.7398 (pt0) REVERT: F 61 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7356 (mt-10) REVERT: G 10 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6748 (mm-30) REVERT: G 119 PHE cc_start: 0.6701 (t80) cc_final: 0.6494 (t80) REVERT: H 36 LYS cc_start: 0.7793 (tppt) cc_final: 0.7548 (mmmt) REVERT: I 108 MET cc_start: 0.7880 (tpp) cc_final: 0.7636 (mmp) REVERT: K 41 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7863 (t) REVERT: K 112 LYS cc_start: 0.8194 (mmmm) cc_final: 0.7875 (mmmm) REVERT: M 565 MET cc_start: 0.7666 (tpp) cc_final: 0.7359 (tpp) REVERT: M 587 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8338 (m) REVERT: M 1130 ILE cc_start: 0.7868 (mm) cc_final: 0.7665 (mm) REVERT: M 1234 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7795 (tttm) REVERT: M 1293 LEU cc_start: 0.7713 (tp) cc_final: 0.7122 (tp) REVERT: N 573 TRP cc_start: 0.6911 (OUTLIER) cc_final: 0.4962 (t60) REVERT: N 674 MET cc_start: 0.8112 (tpp) cc_final: 0.7494 (mtp) REVERT: N 728 MET cc_start: 0.7354 (mmt) cc_final: 0.7106 (tpp) REVERT: N 769 PHE cc_start: 0.8366 (t80) cc_final: 0.8074 (t80) REVERT: N 848 LEU cc_start: 0.8016 (mt) cc_final: 0.7676 (mp) REVERT: O 101 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6578 (m-10) REVERT: R 90 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8203 (mt) REVERT: S 140 ASP cc_start: 0.8173 (t0) cc_final: 0.7900 (t0) REVERT: U 73 SER cc_start: 0.8805 (p) cc_final: 0.8514 (t) REVERT: V 12 LYS cc_start: 0.7873 (tptt) cc_final: 0.7618 (tptp) REVERT: X 43 ILE cc_start: 0.6872 (mt) cc_final: 0.6536 (mt) REVERT: X 44 MET cc_start: 0.6068 (mpp) cc_final: 0.5483 (mmt) outliers start: 176 outliers final: 141 residues processed: 764 average time/residue: 0.4990 time to fit residues: 661.2264 Evaluate side-chains 762 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 611 time to evaluate : 4.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 587 THR Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 636 ILE Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1045 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1163 HIS Chi-restraints excluded: chain M residue 1284 PHE Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1371 ILE Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 526 LEU Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 596 ILE Chi-restraints excluded: chain N residue 598 VAL Chi-restraints excluded: chain N residue 667 THR Chi-restraints excluded: chain N residue 692 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 752 TYR Chi-restraints excluded: chain N residue 866 ILE Chi-restraints excluded: chain N residue 870 THR Chi-restraints excluded: chain N residue 928 ILE Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 101 PHE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 40 PHE Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 594 optimal weight: 10.0000 chunk 391 optimal weight: 0.7980 chunk 630 optimal weight: 3.9990 chunk 384 optimal weight: 0.6980 chunk 299 optimal weight: 0.3980 chunk 438 optimal weight: 0.4980 chunk 661 optimal weight: 7.9990 chunk 608 optimal weight: 4.9990 chunk 526 optimal weight: 0.0000 chunk 54 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS F 72 GLN ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN O 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 55352 Z= 0.175 Angle : 0.623 16.035 74786 Z= 0.306 Chirality : 0.044 0.374 8362 Planarity : 0.004 0.071 9702 Dihedral : 4.000 40.018 7396 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.59 % Allowed : 20.48 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.41 (0.10), residues: 6690 helix: 1.15 (0.11), residues: 2336 sheet: -0.07 (0.16), residues: 918 loop : -0.16 (0.11), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 236 HIS 0.019 0.001 HIS C 265 PHE 0.022 0.001 PHE M 397 TYR 0.033 0.001 TYR L 41 ARG 0.011 0.000 ARG M 954 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 652 time to evaluate : 5.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.4530 (tmm) cc_final: 0.3568 (ttp) REVERT: A 875 TYR cc_start: 0.7662 (m-80) cc_final: 0.7374 (m-80) REVERT: A 962 ASP cc_start: 0.7578 (m-30) cc_final: 0.7247 (m-30) REVERT: A 1130 ILE cc_start: 0.7827 (mm) cc_final: 0.7613 (mm) REVERT: A 1292 MET cc_start: 0.7963 (ppp) cc_final: 0.7662 (ppp) REVERT: A 1293 LEU cc_start: 0.7287 (tp) cc_final: 0.7016 (tp) REVERT: A 1484 MET cc_start: 0.6520 (pmm) cc_final: 0.6051 (pmm) REVERT: B 119 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7984 (p) REVERT: B 276 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7262 (mm) REVERT: B 388 TYR cc_start: 0.6704 (m-80) cc_final: 0.6371 (m-80) REVERT: B 531 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7146 (p90) REVERT: B 553 LEU cc_start: 0.6294 (mt) cc_final: 0.3744 (mt) REVERT: B 573 TRP cc_start: 0.6922 (OUTLIER) cc_final: 0.5318 (t60) REVERT: B 733 MET cc_start: 0.7822 (ppp) cc_final: 0.7431 (ptm) REVERT: B 802 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6967 (t0) REVERT: B 848 LEU cc_start: 0.7977 (mt) cc_final: 0.7661 (mp) REVERT: B 983 GLU cc_start: 0.6352 (tt0) cc_final: 0.5925 (pt0) REVERT: C 131 THR cc_start: 0.6952 (p) cc_final: 0.6717 (p) REVERT: D 36 GLU cc_start: 0.7291 (tp30) cc_final: 0.7017 (tp30) REVERT: F 61 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7644 (mt-10) REVERT: H 36 LYS cc_start: 0.7858 (tppt) cc_final: 0.7611 (mmmt) REVERT: I 108 MET cc_start: 0.7842 (tpp) cc_final: 0.7595 (mmp) REVERT: K 41 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7814 (t) REVERT: K 112 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7804 (mmmm) REVERT: M 561 MET cc_start: 0.7515 (mmt) cc_final: 0.7175 (mmt) REVERT: M 565 MET cc_start: 0.7564 (tpp) cc_final: 0.7302 (tpp) REVERT: M 587 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8290 (m) REVERT: M 1130 ILE cc_start: 0.7686 (mm) cc_final: 0.7410 (mm) REVERT: M 1234 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7785 (tttm) REVERT: M 1293 LEU cc_start: 0.7761 (tp) cc_final: 0.7197 (tp) REVERT: N 573 TRP cc_start: 0.6828 (OUTLIER) cc_final: 0.4880 (t60) REVERT: N 674 MET cc_start: 0.8050 (tpp) cc_final: 0.7401 (mtp) REVERT: N 728 MET cc_start: 0.7295 (mmt) cc_final: 0.7040 (tpp) REVERT: N 848 LEU cc_start: 0.7948 (mt) cc_final: 0.7628 (mp) REVERT: O 101 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6718 (m-10) REVERT: Q 72 MET cc_start: 0.5010 (mmm) cc_final: 0.4575 (mmp) REVERT: R 90 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8158 (mt) REVERT: S 140 ASP cc_start: 0.8166 (t0) cc_final: 0.7945 (t0) REVERT: S 164 MET cc_start: 0.8094 (ppp) cc_final: 0.7633 (ppp) REVERT: U 73 SER cc_start: 0.8768 (p) cc_final: 0.8456 (t) REVERT: V 12 LYS cc_start: 0.7797 (tptt) cc_final: 0.7535 (tptp) REVERT: W 42 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7316 (mm) REVERT: W 45 ILE cc_start: 0.7786 (mm) cc_final: 0.7248 (mm) REVERT: X 43 ILE cc_start: 0.6819 (mt) cc_final: 0.6514 (mt) REVERT: X 44 MET cc_start: 0.6100 (mpp) cc_final: 0.5535 (mmt) outliers start: 156 outliers final: 128 residues processed: 770 average time/residue: 0.5273 time to fit residues: 712.0092 Evaluate side-chains 754 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 615 time to evaluate : 5.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 531 TYR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 587 THR Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain M residue 636 ILE Chi-restraints excluded: chain M residue 872 MET Chi-restraints excluded: chain M residue 955 GLU Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1045 LEU Chi-restraints excluded: chain M residue 1158 LEU Chi-restraints excluded: chain M residue 1163 HIS Chi-restraints excluded: chain M residue 1284 PHE Chi-restraints excluded: chain M residue 1291 ASN Chi-restraints excluded: chain M residue 1320 ILE Chi-restraints excluded: chain M residue 1322 ILE Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1371 ILE Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 487 SER Chi-restraints excluded: chain N residue 522 LEU Chi-restraints excluded: chain N residue 526 LEU Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 598 VAL Chi-restraints excluded: chain N residue 692 THR Chi-restraints excluded: chain N residue 697 GLU Chi-restraints excluded: chain N residue 752 TYR Chi-restraints excluded: chain N residue 866 ILE Chi-restraints excluded: chain N residue 870 THR Chi-restraints excluded: chain N residue 928 ILE Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 101 PHE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 ILE Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain Q residue 22 HIS Chi-restraints excluded: chain Q residue 40 PHE Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 117 SER Chi-restraints excluded: chain T residue 130 ASN Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 42 LEU Chi-restraints excluded: chain W residue 70 LYS Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 101 LEU Chi-restraints excluded: chain W residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 322 optimal weight: 2.9990 chunk 418 optimal weight: 20.0000 chunk 561 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 485 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 146 optimal weight: 0.0070 chunk 527 optimal weight: 0.5980 chunk 220 optimal weight: 9.9990 chunk 541 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 HIS ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 731 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS C 32 ASN C 265 HIS F 72 GLN G 21 ASN ** M 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 731 GLN ** N 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS P 19 GLN Q 132 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.128492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.106741 restraints weight = 140417.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.106738 restraints weight = 90111.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.107587 restraints weight = 74733.087| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 55352 Z= 0.307 Angle : 0.685 15.360 74786 Z= 0.341 Chirality : 0.046 0.392 8362 Planarity : 0.005 0.070 9702 Dihedral : 4.236 39.542 7396 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.81 % Allowed : 20.40 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.10), residues: 6690 helix: 1.08 (0.11), residues: 2316 sheet: -0.10 (0.16), residues: 924 loop : -0.23 (0.11), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 176 HIS 0.036 0.002 HIS B 144 PHE 0.035 0.002 PHE N 956 TYR 0.032 0.002 TYR L 41 ARG 0.011 0.001 ARG M 954 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13555.02 seconds wall clock time: 245 minutes 24.56 seconds (14724.56 seconds total)