Starting phenix.real_space_refine on Sat Feb 24 03:28:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bws_16299/02_2024/8bws_16299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bws_16299/02_2024/8bws_16299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bws_16299/02_2024/8bws_16299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bws_16299/02_2024/8bws_16299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bws_16299/02_2024/8bws_16299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bws_16299/02_2024/8bws_16299_updated.pdb" } resolution = 3.2 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 51 5.49 5 Mg 1 5.21 5 S 209 5.16 5 C 25860 2.51 5 N 7061 2.21 5 O 7825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41013 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1424, 11145 Classifications: {'peptide': 1424} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1359} Chain breaks: 3 Chain: "B" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8715 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 41, 'TRANS': 1062} Chain breaks: 1 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1169 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1569 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 381 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1492 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "O" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4558 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1134 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain breaks: 1 Chain: "S" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 402 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "T" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 492 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 158 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '4QM': 1} 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 492 SG CYS A 67 39.509 73.456 88.870 1.00 71.64 S ATOM 510 SG CYS A 70 41.684 72.227 89.360 1.00 71.31 S ATOM 557 SG CYS A 77 42.116 75.442 90.906 1.00 62.68 S ATOM 795 SG CYS A 107 71.909 99.976 60.939 1.00 59.20 S ATOM 818 SG CYS A 110 70.524 98.303 58.520 1.00 58.97 S ATOM 1184 SG CYS A 154 71.744 101.851 59.643 1.00 73.06 S ATOM 1208 SG CYS A 157 70.631 100.989 57.240 1.00 69.09 S ATOM 19433 SG CYS B1095 56.972 69.047 80.531 1.00 54.99 S ATOM 19456 SG CYS B1098 56.816 72.692 78.998 1.00 55.28 S ATOM 19522 SG CYS B1107 54.112 70.589 80.419 1.00 66.13 S ATOM 19542 SG CYS B1110 55.944 70.094 76.975 1.00 74.74 S ATOM 28825 SG CYS I 5 77.563 156.760 89.477 1.00127.03 S ATOM 28844 SG CYS I 8 73.617 156.371 88.362 1.00122.82 S ATOM 28972 SG CYS I 26 78.845 155.595 87.993 1.00136.92 S ATOM 28995 SG CYS I 29 76.422 156.955 85.372 1.00139.84 S ATOM 29272 SG CYS J 7 50.153 92.917 157.725 1.00 42.55 S ATOM 29295 SG CYS J 10 53.136 91.111 160.599 1.00 47.26 S ATOM 29575 SG CYS J 45 53.080 93.511 159.460 1.00 48.24 S ATOM 29581 SG CYS J 46 49.744 93.885 161.372 1.00 47.08 S ATOM 30632 SG CYS L 31 16.020 104.659 133.358 1.00 87.43 S ATOM 30652 SG CYS L 34 13.772 104.517 135.395 1.00 90.94 S ATOM 30756 SG CYS L 48 12.821 103.697 132.838 1.00 97.59 S ATOM 30779 SG CYS L 51 14.158 107.847 133.158 1.00100.57 S Time building chain proxies: 21.88, per 1000 atoms: 0.53 Number of scatterers: 41013 At special positions: 0 Unit cell: (141.075, 194.94, 200.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 209 16.00 P 51 15.00 Mg 1 11.99 O 7825 8.00 N 7061 7.00 C 25860 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 - 3.50 Amino acid : False - 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: 16.10 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb=" ZN I2002 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 29 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2002 " - pdb=" SG CYS I 8 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L2001 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 31 " Number of angles added : 33 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9476 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 45 sheets defined 34.3% alpha, 10.6% beta 21 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 20.27 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 192 through 207 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.583A pdb=" N GLU A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.922A pdb=" N GLN A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 256 removed outlier: 3.688A pdb=" N TYR A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 284 through 305 removed outlier: 3.607A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 363 through 366 No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 677 through 708 Proline residue: A 687 - end of helix removed outlier: 3.789A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 747 removed outlier: 3.944A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 784 Processing helix chain 'A' and resid 790 through 796 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 858 through 892 removed outlier: 4.726A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 923 through 925 No H-bonds generated for 'chain 'A' and resid 923 through 925' Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 956 through 966 Processing helix chain 'A' and resid 969 through 972 No H-bonds generated for 'chain 'A' and resid 969 through 972' Processing helix chain 'A' and resid 999 through 1026 removed outlier: 3.665A pdb=" N ARG A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1059 Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1089 through 1098 Processing helix chain 'A' and resid 1100 through 1103 Processing helix chain 'A' and resid 1123 through 1131 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.527A pdb=" N VAL A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1202 through 1214 removed outlier: 4.862A pdb=" N LYS A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1265 Processing helix chain 'A' and resid 1287 through 1289 No H-bonds generated for 'chain 'A' and resid 1287 through 1289' Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1319 through 1326 Processing helix chain 'A' and resid 1329 through 1345 Processing helix chain 'A' and resid 1352 through 1362 Processing helix chain 'A' and resid 1373 through 1377 removed outlier: 3.746A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1373 through 1377' Processing helix chain 'A' and resid 1383 through 1389 Processing helix chain 'A' and resid 1392 through 1401 Processing helix chain 'A' and resid 1411 through 1417 Processing helix chain 'A' and resid 1424 through 1426 No H-bonds generated for 'chain 'A' and resid 1424 through 1426' Processing helix chain 'B' and resid 40 through 54 removed outlier: 6.058A pdb=" N TRP B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 60 through 79 removed outlier: 4.992A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 170 through 173 No H-bonds generated for 'chain 'B' and resid 170 through 173' Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.531A pdb=" N ASP B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 380 through 407 Processing helix chain 'B' and resid 421 through 439 removed outlier: 4.257A pdb=" N ASN B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.565A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 626 through 632 Processing helix chain 'B' and resid 639 through 642 No H-bonds generated for 'chain 'B' and resid 639 through 642' Processing helix chain 'B' and resid 653 through 656 Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 677 through 680 removed outlier: 3.773A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 677 through 680' Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 739 through 743 removed outlier: 3.915A pdb=" N LEU B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 739 through 743' Processing helix chain 'B' and resid 778 through 781 No H-bonds generated for 'chain 'B' and resid 778 through 781' Processing helix chain 'B' and resid 946 through 950 removed outlier: 3.576A pdb=" N PHE B 949 " --> pdb=" O PRO B 946 " (cutoff:3.500A) Proline residue: B 950 - end of helix No H-bonds generated for 'chain 'B' and resid 946 through 950' Processing helix chain 'B' and resid 955 through 970 Processing helix chain 'B' and resid 984 through 993 Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1064 through 1073 Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1123 through 1134 Processing helix chain 'C' and resid 36 through 39 No H-bonds generated for 'chain 'C' and resid 36 through 39' Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.971A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.665A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 310 through 330 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 53 through 66 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 141 through 144 No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'E' and resid 2 through 25 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 185 through 188 No H-bonds generated for 'chain 'E' and resid 185 through 188' Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.874A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 81 removed outlier: 4.036A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 141 Processing helix chain 'M' and resid 133 through 139 removed outlier: 3.893A pdb=" N GLU M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 194 Processing helix chain 'M' and resid 230 through 238 Processing helix chain 'M' and resid 253 through 259 Processing helix chain 'M' and resid 274 through 279 Processing helix chain 'N' and resid 275 through 298 removed outlier: 3.590A pdb=" N ASN N 298 " --> pdb=" O LEU N 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 34 removed outlier: 4.342A pdb=" N THR O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 59 through 70 Processing helix chain 'O' and resid 76 through 81 Processing helix chain 'O' and resid 88 through 100 Processing helix chain 'O' and resid 124 through 131 Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 153 through 166 Processing helix chain 'O' and resid 171 through 177 Processing helix chain 'O' and resid 181 through 197 Processing helix chain 'O' and resid 205 through 208 Processing helix chain 'O' and resid 211 through 219 Processing helix chain 'O' and resid 234 through 257 removed outlier: 3.708A pdb=" N THR O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP O 248 " --> pdb=" O ASN O 244 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 284 through 302 removed outlier: 3.709A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 Processing helix chain 'O' and resid 341 through 355 Processing helix chain 'O' and resid 363 through 369 Processing helix chain 'O' and resid 450 through 462 Processing helix chain 'O' and resid 481 through 499 Proline residue: O 485 - end of helix Processing helix chain 'O' and resid 502 through 513 Processing helix chain 'O' and resid 519 through 526 Processing helix chain 'O' and resid 530 through 541 Processing helix chain 'O' and resid 570 through 598 Processing helix chain 'O' and resid 600 through 607 removed outlier: 3.776A pdb=" N ASN O 607 " --> pdb=" O LEU O 603 " (cutoff:3.500A) Processing helix chain 'O' and resid 615 through 618 No H-bonds generated for 'chain 'O' and resid 615 through 618' Processing helix chain 'O' and resid 621 through 652 removed outlier: 4.960A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 189 Processing helix chain 'P' and resid 195 through 197 No H-bonds generated for 'chain 'P' and resid 195 through 197' Processing helix chain 'P' and resid 218 through 228 Processing helix chain 'P' and resid 237 through 248 Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.867A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 298 removed outlier: 5.354A pdb=" N PHE P 297 " --> pdb=" O PHE P 294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 44 No H-bonds generated for 'chain 'Q' and resid 42 through 44' Processing helix chain 'Q' and resid 49 through 67 removed outlier: 3.951A pdb=" N PHE Q 61 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY Q 62 " --> pdb=" O TYR Q 58 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 138 removed outlier: 4.027A pdb=" N ASN Q 138 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.429A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 376 through 380 Processing sheet with id= D, first strand: chain 'A' and resid 381 through 383 removed outlier: 5.994A pdb=" N PHE A 498 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 403 through 407 Processing sheet with id= F, first strand: chain 'A' and resid 626 through 628 removed outlier: 6.760A pdb=" N ARG A 655 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 896 through 898 Processing sheet with id= H, first strand: chain 'A' and resid 1314 through 1316 removed outlier: 3.746A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1173 through 1177 removed outlier: 4.467A pdb=" N SER A1182 " --> pdb=" O VAL A1234 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.940A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE B 133 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASP B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR B 135 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS B 144 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= L, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= M, first strand: chain 'B' and resid 589 through 593 removed outlier: 6.895A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU B 557 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 609 through 613 Processing sheet with id= O, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.896A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 753 through 759 removed outlier: 4.141A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 846 through 848 Processing sheet with id= R, first strand: chain 'B' and resid 1090 through 1095 Processing sheet with id= S, first strand: chain 'B' and resid 771 through 774 removed outlier: 7.169A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 41 through 44 removed outlier: 4.057A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 303 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 132 through 139 removed outlier: 3.844A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= W, first strand: chain 'C' and resid 161 through 163 Processing sheet with id= X, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.958A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.399A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.793A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AB, first strand: chain 'G' and resid 7 through 13 Processing sheet with id= AC, first strand: chain 'G' and resid 85 through 87 Processing sheet with id= AD, first strand: chain 'G' and resid 97 through 99 removed outlier: 4.023A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 44 through 48 removed outlier: 4.235A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 149 through 155 removed outlier: 6.913A pdb=" N LEU G 197 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU G 153 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA G 195 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 100 through 106 removed outlier: 6.890A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG H 25 " --> pdb=" O ASP H 16 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP H 16 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AI, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.754A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AK, first strand: chain 'M' and resid 76 through 78 removed outlier: 6.135A pdb=" N VAL M 168 " --> pdb=" O LYS M 77 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 87 through 90 removed outlier: 4.490A pdb=" N GLN M 178 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL M 151 " --> pdb=" O GLN M 178 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN M 146 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE M 123 " --> pdb=" O GLN M 146 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA M 110 " --> pdb=" O LEU M 245 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 306 through 308 Processing sheet with id= AN, first strand: chain 'N' and resid 363 through 366 removed outlier: 3.788A pdb=" N LYS N 370 " --> pdb=" O HIS N 366 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'O' and resid 104 through 109 removed outlier: 3.507A pdb=" N LYS O 105 " --> pdb=" O TYR O 121 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'O' and resid 200 through 202 Processing sheet with id= AQ, first strand: chain 'O' and resid 547 through 551 Processing sheet with id= AR, first strand: chain 'O' and resid 469 through 472 removed outlier: 6.701A pdb=" N VAL O 475 " --> pdb=" O THR O 471 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'P' and resid 254 through 256 1295 hydrogen bonds defined for protein. 3690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 18.64 Time building geometry restraints manager: 17.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6816 1.31 - 1.44: 10611 1.44 - 1.56: 23995 1.56 - 1.69: 99 1.69 - 1.81: 340 Bond restraints: 41861 Sorted by residual: bond pdb=" CA SER J 9 " pdb=" CB SER J 9 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.58e-02 4.01e+03 1.64e+01 bond pdb=" C PRO B 503 " pdb=" O PRO B 503 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" C LYS J 12 " pdb=" N VAL J 13 " ideal model delta sigma weight residual 1.332 1.300 0.032 9.20e-03 1.18e+04 1.19e+01 bond pdb=" N VAL B 216 " pdb=" CA VAL B 216 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" N TYR G 121 " pdb=" CA TYR G 121 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.15e-02 7.56e+03 1.04e+01 ... (remaining 41856 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.33: 1024 105.33 - 112.52: 21764 112.52 - 119.71: 14283 119.71 - 126.90: 19191 126.90 - 134.09: 498 Bond angle restraints: 56760 Sorted by residual: angle pdb=" N PHE Q 61 " pdb=" CA PHE Q 61 " pdb=" C PHE Q 61 " ideal model delta sigma weight residual 110.35 101.27 9.08 1.36e+00 5.41e-01 4.45e+01 angle pdb=" N LYS Q 57 " pdb=" CA LYS Q 57 " pdb=" C LYS Q 57 " ideal model delta sigma weight residual 113.20 106.22 6.98 1.21e+00 6.83e-01 3.33e+01 angle pdb=" N TYR Q 58 " pdb=" CA TYR Q 58 " pdb=" C TYR Q 58 " ideal model delta sigma weight residual 113.88 106.93 6.95 1.23e+00 6.61e-01 3.19e+01 angle pdb=" CA PHE J 8 " pdb=" CB PHE J 8 " pdb=" CG PHE J 8 " ideal model delta sigma weight residual 113.80 118.89 -5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" N ALA B 507 " pdb=" CA ALA B 507 " pdb=" C ALA B 507 " ideal model delta sigma weight residual 111.87 105.03 6.84 1.41e+00 5.03e-01 2.36e+01 ... (remaining 56755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.35: 25022 31.35 - 62.70: 650 62.70 - 94.05: 37 94.05 - 125.40: 0 125.40 - 156.75: 2 Dihedral angle restraints: 25711 sinusoidal: 11066 harmonic: 14645 Sorted by residual: dihedral pdb=" CA GLU B 249 " pdb=" C GLU B 249 " pdb=" N GLU B 250 " pdb=" CA GLU B 250 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA HIS B 595 " pdb=" C HIS B 595 " pdb=" N GLN B 596 " pdb=" CA GLN B 596 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLY A 968 " pdb=" C GLY A 968 " pdb=" N PRO A 969 " pdb=" CA PRO A 969 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 25708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 6320 0.116 - 0.231: 102 0.231 - 0.347: 1 0.347 - 0.463: 2 0.463 - 0.579: 5 Chirality restraints: 6430 Sorted by residual: chirality pdb=" P DG S 37 " pdb=" OP1 DG S 37 " pdb=" OP2 DG S 37 " pdb=" O5' DG S 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" P DT T 15 " pdb=" OP1 DT T 15 " pdb=" OP2 DT T 15 " pdb=" O5' DT T 15 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" P DT T 13 " pdb=" OP1 DT T 13 " pdb=" OP2 DT T 13 " pdb=" O5' DT T 13 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.73e+00 ... (remaining 6427 not shown) Planarity restraints: 7105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 227 " 0.444 9.50e-02 1.11e+02 1.99e-01 2.42e+01 pdb=" NE ARG B 227 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 227 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 227 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 227 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 120 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C TYR G 120 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR G 120 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR G 121 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 556 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.55e+00 pdb=" C ASP A 556 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP A 556 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE A 557 " 0.018 2.00e-02 2.50e+03 ... (remaining 7102 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 284 2.50 - 3.10: 30694 3.10 - 3.70: 63423 3.70 - 4.30: 91604 4.30 - 4.90: 152602 Nonbonded interactions: 338607 Sorted by model distance: nonbonded pdb=" CB ASP A 511 " pdb="MG MG A1503 " model vdw 1.905 2.570 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A1503 " model vdw 2.065 2.170 nonbonded pdb=" O3' A R 10 " pdb="MG MG A1503 " model vdw 2.067 2.170 nonbonded pdb=" OD2 ASP A 511 " pdb="MG MG A1503 " model vdw 2.107 2.170 nonbonded pdb=" OD2 ASP A 513 " pdb="MG MG A1503 " model vdw 2.120 2.170 ... (remaining 338602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 9.670 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: 0.040 Extract box with map and model: 28.260 Check model and map are aligned: 0.680 Set scattering table: 0.400 Process input model: 125.800 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.004 0.064 41861 Z= 0.234 Angle : 0.594 11.954 56760 Z= 0.341 Chirality : 0.046 0.579 6430 Planarity : 0.005 0.199 7105 Dihedral : 13.186 156.745 16235 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.44 % Rotamer: Outliers : 3.98 % Allowed : 7.50 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4959 helix: 1.03 (0.13), residues: 1826 sheet: -0.78 (0.21), residues: 585 loop : -1.35 (0.13), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 146 HIS 0.004 0.001 HIS A 427 PHE 0.017 0.001 PHE F 143 TYR 0.022 0.001 TYR B 232 ARG 0.004 0.000 ARG O 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 669 time to evaluate : 4.679 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7204 (mmp80) cc_final: 0.6988 (mmp80) REVERT: A 219 MET cc_start: 0.8347 (mmt) cc_final: 0.7984 (mmm) REVERT: A 269 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7918 (ptt-90) REVERT: A 889 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7968 (tt) REVERT: A 1333 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7089 (m-10) REVERT: B 42 GLN cc_start: 0.7794 (mt0) cc_final: 0.7543 (mp10) REVERT: B 67 TYR cc_start: 0.7159 (t80) cc_final: 0.6931 (t80) REVERT: B 221 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8658 (t) REVERT: B 234 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8643 (pt) REVERT: B 263 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5351 (pp) REVERT: C 55 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: C 130 ASN cc_start: 0.8831 (t0) cc_final: 0.8429 (t0) REVERT: C 172 GLN cc_start: 0.8321 (mp10) cc_final: 0.7521 (mp10) REVERT: D 1 MET cc_start: 0.6399 (tpt) cc_final: 0.5760 (tpt) REVERT: E 54 GLN cc_start: 0.6347 (pp30) cc_final: 0.5113 (pm20) REVERT: E 146 HIS cc_start: 0.8162 (m170) cc_final: 0.7815 (m170) REVERT: G 130 TRP cc_start: 0.5964 (t60) cc_final: 0.5699 (t60) REVERT: I 32 GLU cc_start: 0.6287 (tp30) cc_final: 0.5957 (pp20) REVERT: J 1 MET cc_start: 0.6888 (mtp) cc_final: 0.6606 (mtp) REVERT: K 123 ASP cc_start: 0.8307 (m-30) cc_final: 0.8078 (m-30) REVERT: M 251 THR cc_start: 0.7243 (t) cc_final: 0.7003 (m) REVERT: M 275 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6488 (tm-30) REVERT: O 577 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7446 (mtp) REVERT: O 585 MET cc_start: 0.7897 (mtp) cc_final: 0.7596 (mtp) REVERT: O 624 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.6980 (tt) REVERT: O 635 LEU cc_start: 0.8536 (tp) cc_final: 0.8298 (mm) REVERT: P 296 TYR cc_start: 0.8434 (p90) cc_final: 0.7774 (p90) REVERT: Q 57 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7370 (mtpt) REVERT: Q 70 PHE cc_start: 0.8336 (m-80) cc_final: 0.8097 (m-10) outliers start: 176 outliers final: 68 residues processed: 811 average time/residue: 0.5102 time to fit residues: 684.1751 Evaluate side-chains 590 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 512 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 503 PRO Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 26 CYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 419 optimal weight: 3.9990 chunk 376 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 389 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 289 optimal weight: 0.0570 chunk 451 optimal weight: 5.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 320 GLN A 625 ASN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1174 GLN ** A1318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS B 286 ASN B 362 ASN B 456 HIS B 493 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B 837 GLN B 840 GLN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B1014 GLN C 207 HIS D 56 GLN D 71 ASN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN H 134 ASN J 23 ASN K 118 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN N 289 HIS ** O 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 631 ASN P 219 GLN P 239 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41861 Z= 0.310 Angle : 0.586 13.219 56760 Z= 0.301 Chirality : 0.043 0.178 6430 Planarity : 0.004 0.062 7105 Dihedral : 11.693 157.435 6358 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.36 % Favored : 92.62 % Rotamer: Outliers : 3.93 % Allowed : 11.68 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4959 helix: 0.87 (0.12), residues: 1829 sheet: -0.72 (0.21), residues: 609 loop : -1.38 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 201 HIS 0.007 0.001 HIS A 427 PHE 0.029 0.001 PHE B 678 TYR 0.026 0.002 TYR D 50 ARG 0.006 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 539 time to evaluate : 5.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: A 219 MET cc_start: 0.8227 (mmt) cc_final: 0.7958 (mmm) REVERT: A 269 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7883 (ptt-90) REVERT: A 890 MET cc_start: 0.8645 (tpp) cc_final: 0.7518 (tpt) REVERT: A 1060 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 1150 ASP cc_start: 0.8125 (p0) cc_final: 0.7878 (p0) REVERT: A 1333 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: B 42 GLN cc_start: 0.7833 (mt0) cc_final: 0.7569 (mp10) REVERT: B 132 ASP cc_start: 0.7588 (m-30) cc_final: 0.7348 (m-30) REVERT: B 239 LYS cc_start: 0.8325 (ptmm) cc_final: 0.8033 (ptmm) REVERT: B 263 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.5352 (pp) REVERT: B 545 ASP cc_start: 0.8395 (p0) cc_final: 0.8181 (p0) REVERT: B 656 ASP cc_start: 0.7078 (t0) cc_final: 0.6822 (t0) REVERT: C 55 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: C 130 ASN cc_start: 0.8914 (t0) cc_final: 0.8459 (t0) REVERT: D 1 MET cc_start: 0.6531 (tpt) cc_final: 0.5921 (tpt) REVERT: E 113 GLN cc_start: 0.8458 (tt0) cc_final: 0.8206 (mt0) REVERT: E 146 HIS cc_start: 0.8202 (m170) cc_final: 0.7862 (m170) REVERT: G 149 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7928 (mtp-110) REVERT: I 32 GLU cc_start: 0.6396 (tp30) cc_final: 0.6072 (pp20) REVERT: J 1 MET cc_start: 0.7046 (mtp) cc_final: 0.6695 (mtp) REVERT: J 27 GLU cc_start: 0.7016 (pm20) cc_final: 0.6214 (pm20) REVERT: K 67 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7018 (mm-30) REVERT: K 123 ASP cc_start: 0.8344 (m-30) cc_final: 0.8071 (m-30) REVERT: M 275 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6567 (tm-30) REVERT: O 240 GLN cc_start: 0.7456 (pp30) cc_final: 0.7221 (tt0) REVERT: O 585 MET cc_start: 0.7919 (mtp) cc_final: 0.7689 (mtp) REVERT: O 624 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.6963 (tt) REVERT: Q 57 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7116 (mtpt) REVERT: Q 108 TYR cc_start: 0.6359 (t80) cc_final: 0.6082 (t80) outliers start: 174 outliers final: 115 residues processed: 673 average time/residue: 0.5167 time to fit residues: 580.8552 Evaluate side-chains 622 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 499 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 250 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 375 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 chunk 452 optimal weight: 3.9990 chunk 488 optimal weight: 0.9980 chunk 402 optimal weight: 1.9990 chunk 448 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 362 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS B 286 ASN B 456 HIS B 550 HIS ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN O 544 ASN P 219 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41861 Z= 0.257 Angle : 0.559 12.542 56760 Z= 0.287 Chirality : 0.042 0.218 6430 Planarity : 0.004 0.058 7105 Dihedral : 11.420 156.358 6330 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.13 % Allowed : 13.17 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4959 helix: 0.85 (0.12), residues: 1840 sheet: -0.81 (0.20), residues: 625 loop : -1.36 (0.13), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 201 HIS 0.006 0.001 HIS B 456 PHE 0.022 0.001 PHE B 678 TYR 0.018 0.001 TYR D 50 ARG 0.004 0.000 ARG P 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 522 time to evaluate : 5.152 Fit side-chains REVERT: A 193 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6820 (pm20) REVERT: A 219 MET cc_start: 0.8213 (mmt) cc_final: 0.7962 (mmm) REVERT: A 269 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7927 (ptt-90) REVERT: A 483 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8178 (mt) REVERT: A 890 MET cc_start: 0.8531 (tpp) cc_final: 0.7926 (tpt) REVERT: A 1060 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7281 (t80) REVERT: A 1333 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: B 42 GLN cc_start: 0.7825 (mt0) cc_final: 0.7570 (mp10) REVERT: B 132 ASP cc_start: 0.7569 (m-30) cc_final: 0.7311 (m-30) REVERT: B 239 LYS cc_start: 0.8261 (ptmm) cc_final: 0.8056 (ptmm) REVERT: B 263 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5357 (pp) REVERT: B 352 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8253 (mtp) REVERT: B 656 ASP cc_start: 0.7167 (t0) cc_final: 0.6929 (t0) REVERT: B 802 THR cc_start: 0.6733 (OUTLIER) cc_final: 0.6443 (p) REVERT: C 55 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: C 130 ASN cc_start: 0.8901 (t0) cc_final: 0.8415 (t0) REVERT: D 1 MET cc_start: 0.6547 (tpt) cc_final: 0.5870 (tpt) REVERT: E 146 HIS cc_start: 0.8198 (m170) cc_final: 0.7865 (m170) REVERT: G 149 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7853 (mtp85) REVERT: H 11 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: J 49 MET cc_start: 0.8376 (tpp) cc_final: 0.8141 (tpp) REVERT: K 67 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6970 (mm-30) REVERT: K 123 ASP cc_start: 0.8330 (m-30) cc_final: 0.8070 (m-30) REVERT: M 275 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6559 (tm-30) REVERT: O 240 GLN cc_start: 0.7477 (pp30) cc_final: 0.7221 (tt0) REVERT: O 624 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.6982 (tt) REVERT: P 245 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8117 (mm-30) REVERT: Q 108 TYR cc_start: 0.6372 (t80) cc_final: 0.6068 (t80) outliers start: 183 outliers final: 131 residues processed: 663 average time/residue: 0.5146 time to fit residues: 573.3799 Evaluate side-chains 631 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 489 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 446 optimal weight: 0.6980 chunk 339 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 303 optimal weight: 0.9980 chunk 453 optimal weight: 0.8980 chunk 480 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN ** A1318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS B 286 ASN B 362 ASN B 550 HIS B 733 GLN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN M 132 ASN N 288 GLN P 219 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41861 Z= 0.244 Angle : 0.553 12.572 56760 Z= 0.283 Chirality : 0.042 0.279 6430 Planarity : 0.004 0.060 7105 Dihedral : 11.329 155.940 6323 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.59 % Allowed : 14.25 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4959 helix: 0.86 (0.12), residues: 1828 sheet: -0.80 (0.20), residues: 615 loop : -1.35 (0.13), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 201 HIS 0.005 0.001 HIS B 456 PHE 0.029 0.001 PHE E 16 TYR 0.014 0.001 TYR D 50 ARG 0.005 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 525 time to evaluate : 4.890 Fit side-chains REVERT: A 193 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: A 219 MET cc_start: 0.8221 (mmt) cc_final: 0.7992 (mmm) REVERT: A 269 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7941 (ptt-90) REVERT: A 483 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8149 (mt) REVERT: A 890 MET cc_start: 0.8216 (tpp) cc_final: 0.7761 (tpt) REVERT: A 1060 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7265 (t80) REVERT: A 1333 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: B 42 GLN cc_start: 0.7844 (mt0) cc_final: 0.7586 (mp10) REVERT: B 132 ASP cc_start: 0.7575 (m-30) cc_final: 0.7355 (m-30) REVERT: B 239 LYS cc_start: 0.8250 (ptmm) cc_final: 0.7971 (ptmm) REVERT: B 263 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5378 (pp) REVERT: B 802 THR cc_start: 0.6745 (OUTLIER) cc_final: 0.6460 (p) REVERT: C 55 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: C 130 ASN cc_start: 0.8924 (t0) cc_final: 0.8430 (t0) REVERT: C 193 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8239 (mp) REVERT: D 1 MET cc_start: 0.6546 (tpt) cc_final: 0.5908 (tpt) REVERT: D 50 TYR cc_start: 0.6742 (t80) cc_final: 0.6336 (t80) REVERT: D 52 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6203 (m170) REVERT: E 146 HIS cc_start: 0.8200 (m170) cc_final: 0.7817 (m170) REVERT: G 149 ARG cc_start: 0.8112 (mtp-110) cc_final: 0.7713 (mtp85) REVERT: G 150 ILE cc_start: 0.8141 (mp) cc_final: 0.7885 (mp) REVERT: H 11 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: J 27 GLU cc_start: 0.6981 (pm20) cc_final: 0.6182 (pm20) REVERT: J 49 MET cc_start: 0.8368 (tpp) cc_final: 0.8121 (tpp) REVERT: K 67 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6948 (mm-30) REVERT: K 123 ASP cc_start: 0.8322 (m-30) cc_final: 0.8057 (m-30) REVERT: M 275 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6539 (tm-30) REVERT: O 240 GLN cc_start: 0.7431 (pp30) cc_final: 0.7084 (tt0) REVERT: O 624 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.6993 (tt) outliers start: 203 outliers final: 151 residues processed: 680 average time/residue: 0.5229 time to fit residues: 599.3168 Evaluate side-chains 667 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 504 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 624 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 400 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 357 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 409 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 chunk 431 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS B 286 ASN B 733 GLN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN N 288 GLN N 421 GLN O 575 ASN P 219 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 41861 Z= 0.357 Angle : 0.602 13.411 56760 Z= 0.308 Chirality : 0.044 0.226 6430 Planarity : 0.004 0.062 7105 Dihedral : 11.357 154.807 6316 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.06 % Allowed : 14.75 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4959 helix: 0.73 (0.12), residues: 1824 sheet: -0.83 (0.20), residues: 618 loop : -1.42 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 201 HIS 0.008 0.001 HIS A 427 PHE 0.024 0.001 PHE B 678 TYR 0.017 0.002 TYR O 185 ARG 0.006 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 514 time to evaluate : 5.128 Fit side-chains REVERT: A 193 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6828 (pm20) REVERT: A 219 MET cc_start: 0.8281 (mmt) cc_final: 0.8040 (mmm) REVERT: A 269 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7879 (ptt-90) REVERT: A 483 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 890 MET cc_start: 0.8436 (tpp) cc_final: 0.7529 (tpt) REVERT: A 1060 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7341 (t80) REVERT: A 1333 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7150 (m-10) REVERT: B 42 GLN cc_start: 0.7866 (mt0) cc_final: 0.7583 (mp10) REVERT: B 132 ASP cc_start: 0.7598 (m-30) cc_final: 0.7365 (m-30) REVERT: B 239 LYS cc_start: 0.8231 (ptmm) cc_final: 0.7950 (ptmm) REVERT: B 263 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5568 (pp) REVERT: B 802 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6480 (p) REVERT: B 1047 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8832 (t) REVERT: C 55 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: C 130 ASN cc_start: 0.8920 (t0) cc_final: 0.8414 (t0) REVERT: C 193 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8304 (mp) REVERT: D 1 MET cc_start: 0.6735 (tpt) cc_final: 0.6032 (tpt) REVERT: D 52 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6392 (m170) REVERT: E 146 HIS cc_start: 0.8285 (m170) cc_final: 0.7936 (m170) REVERT: G 149 ARG cc_start: 0.8092 (mtp-110) cc_final: 0.7802 (mtp85) REVERT: H 11 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: J 49 MET cc_start: 0.8425 (tpp) cc_final: 0.8072 (tpp) REVERT: K 67 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7050 (mm-30) REVERT: K 123 ASP cc_start: 0.8383 (m-30) cc_final: 0.8095 (m-30) REVERT: M 275 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6575 (tm-30) REVERT: Q 108 TYR cc_start: 0.6316 (t80) cc_final: 0.6039 (t80) outliers start: 224 outliers final: 174 residues processed: 679 average time/residue: 0.5094 time to fit residues: 583.9736 Evaluate side-chains 672 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 486 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 421 GLN Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 129 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain Q residue 157 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 161 optimal weight: 2.9990 chunk 432 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 282 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 480 optimal weight: 6.9990 chunk 399 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 844 ASN E 32 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN ** N 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 41861 Z= 0.353 Angle : 0.608 13.998 56760 Z= 0.311 Chirality : 0.044 0.230 6430 Planarity : 0.004 0.064 7105 Dihedral : 11.380 153.588 6314 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.17 % Allowed : 15.77 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4959 helix: 0.67 (0.12), residues: 1819 sheet: -0.84 (0.21), residues: 617 loop : -1.46 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 201 HIS 0.007 0.001 HIS A 427 PHE 0.026 0.001 PHE E 16 TYR 0.025 0.002 TYR M 112 ARG 0.009 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 494 time to evaluate : 4.696 Fit side-chains REVERT: A 193 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: A 219 MET cc_start: 0.8324 (mmt) cc_final: 0.8082 (mmm) REVERT: A 269 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.7967 (ptt-90) REVERT: A 483 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 890 MET cc_start: 0.8551 (tpp) cc_final: 0.7739 (tpt) REVERT: A 1060 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 1228 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6325 (m-30) REVERT: A 1333 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7159 (m-10) REVERT: B 42 GLN cc_start: 0.7875 (mt0) cc_final: 0.7581 (mp10) REVERT: B 132 ASP cc_start: 0.7625 (m-30) cc_final: 0.7400 (m-30) REVERT: B 263 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5454 (pp) REVERT: B 289 GLU cc_start: 0.7587 (mp0) cc_final: 0.7352 (mp0) REVERT: B 330 THR cc_start: 0.8673 (m) cc_final: 0.8166 (p) REVERT: B 802 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6482 (p) REVERT: C 55 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: C 130 ASN cc_start: 0.8928 (t0) cc_final: 0.8422 (t0) REVERT: C 193 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8297 (mp) REVERT: D 1 MET cc_start: 0.6780 (tpt) cc_final: 0.6163 (tpt) REVERT: D 52 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6561 (m170) REVERT: E 146 HIS cc_start: 0.8298 (m170) cc_final: 0.7923 (m170) REVERT: G 149 ARG cc_start: 0.8136 (mtp-110) cc_final: 0.7857 (mtp85) REVERT: J 27 GLU cc_start: 0.7015 (pm20) cc_final: 0.6208 (pm20) REVERT: J 49 MET cc_start: 0.8441 (tpp) cc_final: 0.8072 (tpp) REVERT: K 67 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7070 (mm-30) REVERT: K 123 ASP cc_start: 0.8385 (m-30) cc_final: 0.8090 (m-30) REVERT: M 275 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6577 (tm-30) REVERT: N 380 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6368 (tmm) REVERT: Q 108 TYR cc_start: 0.6399 (t80) cc_final: 0.6121 (t80) outliers start: 229 outliers final: 186 residues processed: 668 average time/residue: 0.4990 time to fit residues: 560.6496 Evaluate side-chains 685 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 487 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 380 MET Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 517 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 129 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain Q residue 157 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 463 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 273 optimal weight: 0.8980 chunk 351 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 404 optimal weight: 0.0870 chunk 268 optimal weight: 2.9990 chunk 479 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS B 286 ASN ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN E 32 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN ** N 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 332 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41861 Z= 0.175 Angle : 0.544 14.371 56760 Z= 0.277 Chirality : 0.042 0.251 6430 Planarity : 0.004 0.062 7105 Dihedral : 11.179 152.670 6311 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.16 % Allowed : 16.90 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4959 helix: 0.86 (0.12), residues: 1822 sheet: -0.68 (0.21), residues: 636 loop : -1.39 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 197 HIS 0.007 0.001 HIS B 334 PHE 0.015 0.001 PHE N 304 TYR 0.021 0.001 TYR M 112 ARG 0.009 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 534 time to evaluate : 5.075 Fit side-chains REVERT: A 193 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: A 219 MET cc_start: 0.8285 (mmt) cc_final: 0.8033 (mmm) REVERT: A 269 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7989 (ptt-90) REVERT: A 483 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8115 (mt) REVERT: A 890 MET cc_start: 0.8494 (tpp) cc_final: 0.7966 (tpt) REVERT: A 1060 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 1228 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6318 (m-30) REVERT: A 1333 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7091 (m-10) REVERT: B 42 GLN cc_start: 0.7835 (mt0) cc_final: 0.7570 (mp10) REVERT: B 132 ASP cc_start: 0.7572 (m-30) cc_final: 0.7359 (m-30) REVERT: B 263 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5378 (pp) REVERT: B 330 THR cc_start: 0.8707 (m) cc_final: 0.8200 (p) REVERT: B 802 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6552 (p) REVERT: B 1078 LEU cc_start: 0.8697 (tt) cc_final: 0.8394 (tt) REVERT: C 130 ASN cc_start: 0.8904 (t0) cc_final: 0.8231 (t0) REVERT: D 1 MET cc_start: 0.6596 (tpt) cc_final: 0.6075 (tpt) REVERT: D 52 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6304 (m170) REVERT: E 52 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7646 (ttm-80) REVERT: E 146 HIS cc_start: 0.8172 (m170) cc_final: 0.7780 (m170) REVERT: G 149 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7844 (mtp85) REVERT: J 27 GLU cc_start: 0.6965 (pm20) cc_final: 0.6160 (pm20) REVERT: J 49 MET cc_start: 0.8271 (tpp) cc_final: 0.8021 (tpp) REVERT: K 67 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6922 (mm-30) REVERT: K 123 ASP cc_start: 0.8338 (m-30) cc_final: 0.8092 (m-30) REVERT: M 275 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6558 (tm-30) REVERT: P 245 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7967 (mm-30) REVERT: P 299 MET cc_start: 0.6767 (mpp) cc_final: 0.6369 (ptp) REVERT: Q 70 PHE cc_start: 0.8336 (m-80) cc_final: 0.8007 (m-10) REVERT: Q 108 TYR cc_start: 0.6345 (t80) cc_final: 0.6053 (t80) outliers start: 184 outliers final: 133 residues processed: 681 average time/residue: 0.5251 time to fit residues: 598.9091 Evaluate side-chains 636 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 493 time to evaluate : 4.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 142 ILE Chi-restraints excluded: chain Q residue 157 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 296 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 286 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 304 optimal weight: 0.1980 chunk 326 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 376 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN A1435 ASN B 286 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN H 11 GLN M 132 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN ** N 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 631 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41861 Z= 0.247 Angle : 0.571 13.635 56760 Z= 0.290 Chirality : 0.043 0.291 6430 Planarity : 0.004 0.061 7105 Dihedral : 11.168 150.475 6308 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.13 % Allowed : 17.19 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4959 helix: 0.86 (0.12), residues: 1824 sheet: -0.68 (0.21), residues: 637 loop : -1.39 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.006 0.001 HIS B 334 PHE 0.020 0.001 PHE B 678 TYR 0.020 0.001 TYR O 106 ARG 0.011 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 508 time to evaluate : 4.820 Fit side-chains REVERT: A 193 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: A 219 MET cc_start: 0.8279 (mmt) cc_final: 0.8029 (mmm) REVERT: A 269 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.7975 (ptt-90) REVERT: A 483 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 890 MET cc_start: 0.8028 (tpp) cc_final: 0.7742 (tpt) REVERT: A 1228 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6290 (m-30) REVERT: A 1333 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7075 (m-10) REVERT: B 42 GLN cc_start: 0.7870 (mt0) cc_final: 0.7581 (mp10) REVERT: B 132 ASP cc_start: 0.7574 (m-30) cc_final: 0.7272 (m-30) REVERT: B 263 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5443 (pp) REVERT: B 330 THR cc_start: 0.8682 (m) cc_final: 0.8178 (p) REVERT: B 802 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6544 (p) REVERT: B 809 MET cc_start: 0.8345 (tpp) cc_final: 0.8016 (tpt) REVERT: B 1047 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8901 (t) REVERT: C 84 TYR cc_start: 0.8711 (m-80) cc_final: 0.8424 (m-80) REVERT: C 130 ASN cc_start: 0.8929 (t0) cc_final: 0.8504 (t0) REVERT: D 1 MET cc_start: 0.6571 (tpt) cc_final: 0.6047 (tpt) REVERT: D 52 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6269 (m170) REVERT: E 52 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7665 (ttm-80) REVERT: E 146 HIS cc_start: 0.8248 (m170) cc_final: 0.7892 (m170) REVERT: G 149 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7886 (mtp85) REVERT: J 27 GLU cc_start: 0.7007 (pm20) cc_final: 0.6127 (pm20) REVERT: J 49 MET cc_start: 0.8356 (tpp) cc_final: 0.8052 (tpp) REVERT: K 67 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6955 (mm-30) REVERT: K 123 ASP cc_start: 0.8358 (m-30) cc_final: 0.8099 (m-30) REVERT: M 275 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6564 (tm-30) REVERT: Q 108 TYR cc_start: 0.6421 (t80) cc_final: 0.6104 (t80) outliers start: 183 outliers final: 148 residues processed: 646 average time/residue: 0.5216 time to fit residues: 565.1972 Evaluate side-chains 655 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 497 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1372 THR Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 136 ILE Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 522 ILE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 603 LEU Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 217 THR Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 435 optimal weight: 9.9990 chunk 458 optimal weight: 6.9990 chunk 418 optimal weight: 0.0970 chunk 446 optimal weight: 0.7980 chunk 268 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 350 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 403 optimal weight: 10.0000 chunk 422 optimal weight: 0.6980 chunk 444 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN B 286 ASN ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 754 ASN B1029 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN ** N 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 41861 Z= 0.161 Angle : 0.551 11.888 56760 Z= 0.279 Chirality : 0.041 0.235 6430 Planarity : 0.004 0.060 7105 Dihedral : 11.066 148.646 6308 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.52 % Allowed : 17.87 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4959 helix: 0.97 (0.12), residues: 1823 sheet: -0.54 (0.21), residues: 621 loop : -1.38 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 197 HIS 0.012 0.001 HIS A 618 PHE 0.026 0.001 PHE D 113 TYR 0.025 0.001 TYR B 304 ARG 0.013 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 516 time to evaluate : 5.172 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6795 (pm20) REVERT: A 219 MET cc_start: 0.8249 (mmt) cc_final: 0.8030 (mmm) REVERT: A 269 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8049 (ptt-90) REVERT: A 483 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 1228 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6404 (m-30) REVERT: A 1333 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: A 1343 MET cc_start: 0.8516 (mtt) cc_final: 0.8163 (mtt) REVERT: B 42 GLN cc_start: 0.7829 (mt0) cc_final: 0.7567 (mp10) REVERT: B 263 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5303 (pp) REVERT: B 325 GLU cc_start: 0.7695 (tp30) cc_final: 0.7128 (tm-30) REVERT: B 330 THR cc_start: 0.8702 (m) cc_final: 0.7938 (p) REVERT: B 340 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6675 (tp) REVERT: B 802 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6608 (p) REVERT: B 1078 LEU cc_start: 0.8682 (tt) cc_final: 0.8270 (tt) REVERT: C 84 TYR cc_start: 0.8627 (m-80) cc_final: 0.8407 (m-80) REVERT: C 130 ASN cc_start: 0.8916 (t0) cc_final: 0.8494 (t0) REVERT: D 1 MET cc_start: 0.6371 (tpt) cc_final: 0.5924 (tpt) REVERT: D 50 TYR cc_start: 0.6519 (t80) cc_final: 0.5932 (t80) REVERT: E 1 MET cc_start: 0.5679 (ppp) cc_final: 0.5446 (ppp) REVERT: E 146 HIS cc_start: 0.8223 (m170) cc_final: 0.7834 (m170) REVERT: G 149 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7895 (mtp85) REVERT: J 27 GLU cc_start: 0.6961 (pm20) cc_final: 0.6119 (pm20) REVERT: K 67 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6861 (mm-30) REVERT: K 123 ASP cc_start: 0.8292 (m-30) cc_final: 0.8051 (m-30) REVERT: M 275 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6512 (tm-30) REVERT: O 368 ARG cc_start: 0.8366 (tmt-80) cc_final: 0.7926 (tmt170) REVERT: P 245 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7930 (mm-30) REVERT: Q 51 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8268 (mm-30) REVERT: Q 70 PHE cc_start: 0.8310 (m-80) cc_final: 0.7956 (m-10) REVERT: Q 108 TYR cc_start: 0.6383 (t80) cc_final: 0.6063 (t80) outliers start: 156 outliers final: 129 residues processed: 638 average time/residue: 0.5508 time to fit residues: 593.7396 Evaluate side-chains 627 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 490 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 522 ILE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 293 optimal weight: 0.9980 chunk 472 optimal weight: 0.8980 chunk 288 optimal weight: 0.6980 chunk 223 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 495 optimal weight: 8.9990 chunk 455 optimal weight: 10.0000 chunk 394 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN B 286 ASN ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN N 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41861 Z= 0.196 Angle : 0.564 14.868 56760 Z= 0.285 Chirality : 0.042 0.260 6430 Planarity : 0.004 0.060 7105 Dihedral : 11.036 145.377 6307 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.41 % Allowed : 18.14 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4959 helix: 0.95 (0.12), residues: 1827 sheet: -0.57 (0.21), residues: 645 loop : -1.36 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 197 HIS 0.020 0.001 HIS A 618 PHE 0.021 0.001 PHE C 315 TYR 0.020 0.001 TYR D 65 ARG 0.014 0.000 ARG A1211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9918 Ramachandran restraints generated. 4959 Oldfield, 0 Emsley, 4959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 498 time to evaluate : 4.666 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: A 219 MET cc_start: 0.8250 (mmt) cc_final: 0.8026 (mmm) REVERT: A 269 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8000 (ptt-90) REVERT: A 483 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 649 ASP cc_start: 0.7659 (t70) cc_final: 0.7390 (t0) REVERT: A 890 MET cc_start: 0.8469 (tpt) cc_final: 0.7997 (tpt) REVERT: A 1033 GLU cc_start: 0.7963 (pm20) cc_final: 0.7673 (mm-30) REVERT: A 1228 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: A 1333 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7062 (m-10) REVERT: A 1343 MET cc_start: 0.8514 (mtt) cc_final: 0.8158 (mtt) REVERT: B 42 GLN cc_start: 0.7820 (mt0) cc_final: 0.7569 (mp10) REVERT: B 263 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5325 (pp) REVERT: B 325 GLU cc_start: 0.7699 (tp30) cc_final: 0.7126 (tm-30) REVERT: B 330 THR cc_start: 0.8684 (m) cc_final: 0.7926 (p) REVERT: B 340 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6664 (tp) REVERT: B 802 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6614 (p) REVERT: B 1078 LEU cc_start: 0.8683 (tt) cc_final: 0.8393 (tt) REVERT: C 84 TYR cc_start: 0.8675 (m-80) cc_final: 0.8459 (m-80) REVERT: C 130 ASN cc_start: 0.8920 (t0) cc_final: 0.8477 (t0) REVERT: D 1 MET cc_start: 0.6385 (tpt) cc_final: 0.5861 (tpt) REVERT: D 50 TYR cc_start: 0.6500 (t80) cc_final: 0.5951 (t80) REVERT: E 1 MET cc_start: 0.5757 (ppp) cc_final: 0.5536 (ppp) REVERT: E 146 HIS cc_start: 0.8245 (m170) cc_final: 0.7865 (m170) REVERT: G 92 CYS cc_start: 0.6781 (t) cc_final: 0.5764 (m) REVERT: G 149 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7904 (mtp85) REVERT: K 67 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6862 (mm-30) REVERT: K 123 ASP cc_start: 0.8316 (m-30) cc_final: 0.8068 (m-30) REVERT: M 275 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6547 (tm-30) REVERT: O 368 ARG cc_start: 0.8372 (tmt-80) cc_final: 0.7914 (tmt170) REVERT: O 543 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: Q 51 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8280 (mm-30) REVERT: Q 70 PHE cc_start: 0.8312 (m-80) cc_final: 0.7966 (m-10) REVERT: Q 108 TYR cc_start: 0.6430 (t80) cc_final: 0.6114 (t80) outliers start: 151 outliers final: 135 residues processed: 615 average time/residue: 0.5078 time to fit residues: 523.0683 Evaluate side-chains 641 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 497 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1172 TYR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1345 ASN Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1018 PHE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 115 LYS Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 519 GLU Chi-restraints excluded: chain O residue 522 ILE Chi-restraints excluded: chain O residue 543 TYR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 571 THR Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 650 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 313 optimal weight: 0.7980 chunk 420 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 363 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 394 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 405 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN N 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.156017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116973 restraints weight = 61520.464| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.55 r_work: 0.3468 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41861 Z= 0.197 Angle : 0.565 18.782 56760 Z= 0.284 Chirality : 0.042 0.287 6430 Planarity : 0.004 0.063 7105 Dihedral : 10.993 138.394 6305 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.57 % Allowed : 18.09 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4959 helix: 0.95 (0.12), residues: 1826 sheet: -0.55 (0.21), residues: 633 loop : -1.35 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.016 0.001 HIS A 618 PHE 0.025 0.001 PHE K 88 TYR 0.020 0.001 TYR B 304 ARG 0.015 0.000 ARG A1211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11699.87 seconds wall clock time: 211 minutes 52.36 seconds (12712.36 seconds total)