Starting phenix.real_space_refine on Sun Jan 19 17:29:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uif_26544/01_2025/7uif_26544.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uif_26544/01_2025/7uif_26544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uif_26544/01_2025/7uif_26544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uif_26544/01_2025/7uif_26544.map" model { file = "/net/cci-nas-00/data/ceres_data/7uif_26544/01_2025/7uif_26544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uif_26544/01_2025/7uif_26544.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 313 5.16 5 C 39981 2.51 5 N 10825 2.21 5 O 12018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 63137 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 11425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1453, 11425 Classifications: {'peptide': 1453} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1386} Chain: "B" Number of atoms: 9336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9336 Classifications: {'peptide': 1172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1120} Chain breaks: 3 Chain: "C" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2133 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1760 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1126 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 1 Chain: "I" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "K" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 929 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 263 Classifications: {'peptide': 35} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 31} Chain: "P" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 861 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "Q" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1033 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "S" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "a" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3008 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 356} Chain breaks: 3 Chain: "d" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1388 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 2 Chain: "f" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1407 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 159} Chain breaks: 2 Chain: "g" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1409 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain breaks: 4 Chain: "h" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 1 Chain: "i" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 709 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 Chain: "j" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "k" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "n" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5139 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 18, 'TRANS': 606} Chain breaks: 6 Chain: "q" Number of atoms: 4182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4182 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 497} Chain breaks: 4 Chain: "r" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1995 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain breaks: 1 Chain: "s" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "t" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1609 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "u" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "v" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 869 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "w" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 871 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Chain: "z" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 6, 'TRANS': 18} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N PRO z 8 " occ=0.70 ... (5 atoms not shown) pdb=" CD PRO z 8 " occ=0.70 residue: pdb=" N SER z 9 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER z 9 " occ=0.70 Time building chain proxies: 25.66, per 1000 atoms: 0.41 Number of scatterers: 63137 At special positions: 0 Unit cell: (226.32, 251.16, 258.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 313 16.00 O 12018 8.00 N 10825 7.00 C 39981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 88 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.65 Conformation dependent library (CDL) restraints added in 6.2 seconds 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14986 Finding SS restraints... Secondary structure from input PDB file: 279 helices and 70 sheets defined 46.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 260 through 281 removed outlier: 3.513A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 305 removed outlier: 3.856A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.567A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.765A pdb=" N LEU A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.695A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.562A pdb=" N VAL A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.764A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 672 through 698 Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.869A pdb=" N LEU A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.831A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.629A pdb=" N ASP A 871 " --> pdb=" O TYR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 903 through 907 removed outlier: 3.989A pdb=" N THR A 907 " --> pdb=" O THR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.894A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.283A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1055 removed outlier: 3.532A pdb=" N ARG A1055 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 removed outlier: 3.609A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix removed outlier: 3.777A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1081 No H-bonds generated for 'chain 'A' and resid 1080 through 1081' Processing helix chain 'A' and resid 1082 through 1093 removed outlier: 3.538A pdb=" N HIS A1085 " --> pdb=" O ASN A1082 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A1086 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA A1090 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A1091 " --> pdb=" O GLY A1088 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A1093 " --> pdb=" O ALA A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.854A pdb=" N ALA A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1175 removed outlier: 3.619A pdb=" N GLU A1168 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.685A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1222 removed outlier: 3.519A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS A1217 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1255 through 1270 removed outlier: 3.935A pdb=" N LYS A1262 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.585A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.957A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1390 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.568A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.669A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.604A pdb=" N ILE B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.899A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.900A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.363A pdb=" N ALA B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.705A pdb=" N LEU B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.561A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.666A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.767A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.817A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.839A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.099A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.706A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.504A pdb=" N HIS B 761 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.713A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 889 through 893 removed outlier: 4.233A pdb=" N LYS B 892 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.761A pdb=" N ALA B1016 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.811A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.502A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1209 removed outlier: 3.777A pdb=" N LYS B1201 " --> pdb=" O PRO B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1223 removed outlier: 3.861A pdb=" N ASP B1223 " --> pdb=" O ARG B1220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1223' Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.689A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 68 removed outlier: 4.002A pdb=" N ILE C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.541A pdb=" N LEU C 80 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.627A pdb=" N TRP C 170 " --> pdb=" O HIS C 167 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.766A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.900A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 271 Processing helix chain 'D' and resid 51 through 78 Processing helix chain 'D' and resid 110 through 115 removed outlier: 4.131A pdb=" N MET D 114 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 115' Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.613A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.894A pdb=" N GLU E 6 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.536A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 123 through 127 removed outlier: 4.368A pdb=" N ILE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.595A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.822A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.641A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.646A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.590A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.734A pdb=" N SER I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.664A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.764A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.540A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.670A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.610A pdb=" N GLU K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.579A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 116 Processing helix chain 'P' and resid 107 through 113 removed outlier: 4.531A pdb=" N ASN P 113 " --> pdb=" O GLU P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 133 Processing helix chain 'Q' and resid 74 through 82 Processing helix chain 'Q' and resid 83 through 88 removed outlier: 3.714A pdb=" N ASN Q 86 " --> pdb=" O ASP Q 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS Q 88 " --> pdb=" O ASN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 247 removed outlier: 3.654A pdb=" N LYS Q 235 " --> pdb=" O PRO Q 231 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Q 246 " --> pdb=" O ASN Q 242 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN Q 247 " --> pdb=" O ILE Q 243 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 138 Processing helix chain 'S' and resid 146 through 163 removed outlier: 4.591A pdb=" N GLU S 163 " --> pdb=" O VAL S 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.652A pdb=" N ILE S 171 " --> pdb=" O PRO S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 208 Processing helix chain 'S' and resid 212 through 221 removed outlier: 3.709A pdb=" N HIS S 216 " --> pdb=" O PRO S 212 " (cutoff:3.500A) Processing helix chain 'S' and resid 224 through 231 Processing helix chain 'S' and resid 238 through 256 Processing helix chain 'a' and resid 7 through 22 Processing helix chain 'a' and resid 27 through 38 Processing helix chain 'a' and resid 102 through 110 Processing helix chain 'a' and resid 114 through 131 Processing helix chain 'a' and resid 163 through 182 removed outlier: 3.802A pdb=" N SER a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS a 173 " --> pdb=" O THR a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 281 No H-bonds generated for 'chain 'a' and resid 279 through 281' Processing helix chain 'a' and resid 297 through 305 Processing helix chain 'a' and resid 331 through 335 Processing helix chain 'a' and resid 336 through 351 removed outlier: 4.256A pdb=" N GLU a 340 " --> pdb=" O ASP a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 361 Processing helix chain 'a' and resid 550 through 566 Processing helix chain 'd' and resid 32 through 40 removed outlier: 3.845A pdb=" N VAL d 40 " --> pdb=" O LYS d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 62 removed outlier: 4.030A pdb=" N GLU d 44 " --> pdb=" O VAL d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 89 removed outlier: 3.560A pdb=" N ALA d 70 " --> pdb=" O ASN d 66 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA d 88 " --> pdb=" O VAL d 84 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU d 89 " --> pdb=" O LYS d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 128 Processing helix chain 'd' and resid 132 through 148 removed outlier: 3.520A pdb=" N ILE d 148 " --> pdb=" O GLN d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 165 removed outlier: 3.680A pdb=" N LEU d 153 " --> pdb=" O ASN d 149 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS d 162 " --> pdb=" O THR d 158 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE d 163 " --> pdb=" O LYS d 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS d 165 " --> pdb=" O SER d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 191 Processing helix chain 'd' and resid 191 through 199 removed outlier: 4.359A pdb=" N MET d 195 " --> pdb=" O GLY d 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 20 Processing helix chain 'f' and resid 26 through 33 removed outlier: 4.389A pdb=" N GLU f 33 " --> pdb=" O ASP f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 56 removed outlier: 3.719A pdb=" N VAL f 45 " --> pdb=" O SER f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 89 through 97 removed outlier: 3.877A pdb=" N TYR f 97 " --> pdb=" O ILE f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 108 removed outlier: 3.660A pdb=" N MET f 101 " --> pdb=" O TYR f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 192 Processing helix chain 'g' and resid 18 through 23 removed outlier: 3.728A pdb=" N PHE g 23 " --> pdb=" O VAL g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 43 Proline residue: g 32 - end of helix Processing helix chain 'g' and resid 112 through 140 Processing helix chain 'g' and resid 141 through 143 No H-bonds generated for 'chain 'g' and resid 141 through 143' Processing helix chain 'g' and resid 144 through 166 removed outlier: 3.640A pdb=" N GLU g 149 " --> pdb=" O GLU g 145 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN g 150 " --> pdb=" O ARG g 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU g 164 " --> pdb=" O HIS g 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR g 165 " --> pdb=" O LEU g 161 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 213 Processing helix chain 'h' and resid 31 through 55 Processing helix chain 'h' and resid 61 through 86 Processing helix chain 'h' and resid 86 through 93 Processing helix chain 'h' and resid 102 through 115 removed outlier: 6.453A pdb=" N SER h 108 " --> pdb=" O THR h 104 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU h 109 " --> pdb=" O SER h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 119 through 134 Processing helix chain 'h' and resid 144 through 170 removed outlier: 3.818A pdb=" N HIS h 170 " --> pdb=" O GLU h 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 79 Processing helix chain 'i' and resid 83 through 108 removed outlier: 3.830A pdb=" N ASN i 108 " --> pdb=" O LEU i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 115 removed outlier: 3.629A pdb=" N LYS i 112 " --> pdb=" O ASN i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 148 removed outlier: 3.500A pdb=" N GLN i 148 " --> pdb=" O TYR i 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 38 Processing helix chain 'j' and resid 42 through 68 Processing helix chain 'j' and resid 80 through 87 Processing helix chain 'j' and resid 94 through 133 Processing helix chain 'j' and resid 136 through 148 Processing helix chain 'k' and resid 3 through 40 removed outlier: 3.523A pdb=" N GLN k 7 " --> pdb=" O PRO k 3 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY k 35 " --> pdb=" O THR k 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU k 36 " --> pdb=" O PHE k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 77 removed outlier: 3.531A pdb=" N PHE k 48 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU k 49 " --> pdb=" O LYS k 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN k 50 " --> pdb=" O PRO k 46 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER k 62 " --> pdb=" O ARG k 58 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR k 63 " --> pdb=" O LEU k 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU k 75 " --> pdb=" O GLN k 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL k 77 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 110 removed outlier: 3.997A pdb=" N ASP k 94 " --> pdb=" O ALA k 90 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR k 95 " --> pdb=" O LEU k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 114 removed outlier: 3.717A pdb=" N SER k 114 " --> pdb=" O PRO k 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 111 through 114' Processing helix chain 'n' and resid 91 through 117 Processing helix chain 'n' and resid 122 through 154 removed outlier: 3.613A pdb=" N LYS n 126 " --> pdb=" O PRO n 122 " (cutoff:3.500A) Processing helix chain 'n' and resid 161 through 191 Processing helix chain 'n' and resid 241 through 260 Processing helix chain 'n' and resid 263 through 267 Processing helix chain 'n' and resid 344 through 359 Processing helix chain 'n' and resid 365 through 393 removed outlier: 3.700A pdb=" N ASN n 391 " --> pdb=" O LEU n 387 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY n 392 " --> pdb=" O LYS n 388 " (cutoff:3.500A) Processing helix chain 'n' and resid 444 through 450 Processing helix chain 'n' and resid 459 through 486 removed outlier: 6.468A pdb=" N GLU n 465 " --> pdb=" O VAL n 461 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY n 466 " --> pdb=" O SER n 462 " (cutoff:3.500A) Processing helix chain 'n' and resid 530 through 542 Processing helix chain 'n' and resid 545 through 571 Processing helix chain 'n' and resid 684 through 711 removed outlier: 4.009A pdb=" N LEU n 696 " --> pdb=" O GLN n 692 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN n 697 " --> pdb=" O ARG n 693 " (cutoff:3.500A) Processing helix chain 'n' and resid 719 through 725 Processing helix chain 'n' and resid 729 through 734 Processing helix chain 'n' and resid 749 through 753 Processing helix chain 'n' and resid 756 through 760 removed outlier: 3.853A pdb=" N LEU n 759 " --> pdb=" O SER n 756 " (cutoff:3.500A) Processing helix chain 'n' and resid 788 through 792 Processing helix chain 'n' and resid 795 through 798 Processing helix chain 'n' and resid 818 through 820 No H-bonds generated for 'chain 'n' and resid 818 through 820' Processing helix chain 'n' and resid 821 through 832 Processing helix chain 'q' and resid 91 through 97 Processing helix chain 'q' and resid 98 through 111 Proline residue: q 104 - end of helix Processing helix chain 'q' and resid 120 through 133 Processing helix chain 'q' and resid 198 through 226 removed outlier: 3.735A pdb=" N GLU q 217 " --> pdb=" O LEU q 213 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER q 218 " --> pdb=" O ALA q 214 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU q 220 " --> pdb=" O ASN q 216 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA q 221 " --> pdb=" O GLU q 217 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU q 222 " --> pdb=" O SER q 218 " (cutoff:3.500A) Processing helix chain 'q' and resid 226 through 233 removed outlier: 3.823A pdb=" N SER q 230 " --> pdb=" O SER q 226 " (cutoff:3.500A) Processing helix chain 'q' and resid 233 through 239 removed outlier: 4.450A pdb=" N SER q 239 " --> pdb=" O SER q 235 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 249 removed outlier: 3.546A pdb=" N VAL q 249 " --> pdb=" O LEU q 245 " (cutoff:3.500A) Processing helix chain 'q' and resid 265 through 316 removed outlier: 4.437A pdb=" N TYR q 269 " --> pdb=" O THR q 265 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE q 270 " --> pdb=" O LYS q 266 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU q 271 " --> pdb=" O LYS q 267 " (cutoff:3.500A) Processing helix chain 'q' and resid 341 through 345 removed outlier: 3.817A pdb=" N GLY q 345 " --> pdb=" O GLU q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 380 through 386 Processing helix chain 'q' and resid 417 through 422 Processing helix chain 'q' and resid 424 through 450 Processing helix chain 'q' and resid 451 through 455 removed outlier: 4.946A pdb=" N SER q 454 " --> pdb=" O LEU q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 497 through 526 removed outlier: 3.640A pdb=" N SER q 526 " --> pdb=" O SER q 522 " (cutoff:3.500A) Processing helix chain 'q' and resid 541 through 566 removed outlier: 4.458A pdb=" N ILE q 545 " --> pdb=" O ILE q 541 " (cutoff:3.500A) Processing helix chain 'q' and resid 593 through 605 removed outlier: 3.567A pdb=" N THR q 597 " --> pdb=" O ASP q 593 " (cutoff:3.500A) Processing helix chain 'q' and resid 606 through 611 Processing helix chain 'q' and resid 666 through 686 Processing helix chain 'r' and resid 15 through 28 Processing helix chain 'r' and resid 71 through 75 Processing helix chain 'r' and resid 86 through 93 removed outlier: 3.606A pdb=" N ILE r 89 " --> pdb=" O ASN r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 109 Processing helix chain 'r' and resid 199 through 208 Processing helix chain 'r' and resid 225 through 227 No H-bonds generated for 'chain 'r' and resid 225 through 227' Processing helix chain 'r' and resid 264 through 282 removed outlier: 3.865A pdb=" N ILE r 268 " --> pdb=" O ASP r 264 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 47 Processing helix chain 's' and resid 64 through 68 Processing helix chain 's' and resid 134 through 148 Processing helix chain 't' and resid 15 through 24 Processing helix chain 't' and resid 83 through 87 removed outlier: 3.872A pdb=" N ILE t 87 " --> pdb=" O ALA t 84 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 95 removed outlier: 3.607A pdb=" N VAL t 92 " --> pdb=" O PRO t 88 " (cutoff:3.500A) Processing helix chain 't' and resid 103 through 111 removed outlier: 3.544A pdb=" N ILE t 107 " --> pdb=" O SER t 103 " (cutoff:3.500A) Processing helix chain 't' and resid 162 through 177 removed outlier: 3.647A pdb=" N ILE t 177 " --> pdb=" O HIS t 173 " (cutoff:3.500A) Processing helix chain 't' and resid 195 through 209 Processing helix chain 'u' and resid 3 through 30 Processing helix chain 'u' and resid 51 through 78 Processing helix chain 'u' and resid 86 through 138 removed outlier: 3.600A pdb=" N GLN u 90 " --> pdb=" O SER u 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 29 Processing helix chain 'v' and resid 46 through 87 removed outlier: 4.072A pdb=" N ALA v 51 " --> pdb=" O GLU v 47 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN v 87 " --> pdb=" O TRP v 83 " (cutoff:3.500A) Processing helix chain 'v' and resid 101 through 119 Processing helix chain 'w' and resid 21 through 33 Processing helix chain 'w' and resid 35 through 45 removed outlier: 3.627A pdb=" N GLN w 45 " --> pdb=" O TYR w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 45 through 51 removed outlier: 4.090A pdb=" N TRP w 49 " --> pdb=" O GLN w 45 " (cutoff:3.500A) Processing helix chain 'w' and resid 51 through 61 removed outlier: 4.166A pdb=" N LYS w 55 " --> pdb=" O SER w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 62 through 66 removed outlier: 4.137A pdb=" N ASN w 66 " --> pdb=" O TYR w 63 " (cutoff:3.500A) Processing helix chain 'w' and resid 68 through 73 removed outlier: 3.530A pdb=" N ILE w 73 " --> pdb=" O SER w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 89 removed outlier: 3.933A pdb=" N PHE w 80 " --> pdb=" O PRO w 76 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS w 83 " --> pdb=" O LEU w 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET w 89 " --> pdb=" O LEU w 85 " (cutoff:3.500A) Processing helix chain 'w' and resid 105 through 126 Proline residue: w 115 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 6.876A pdb=" N TYR B1217 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 17 " --> pdb=" O ARG B1215 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG B1215 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 7.024A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.572A pdb=" N GLN A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.516A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 367 removed outlier: 6.219A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B1104 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.858A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.686A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 567 removed outlier: 5.840A pdb=" N ILE A 565 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR H 98 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU H 27 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.726A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.527A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.872A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 3.545A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1147 through 1154 removed outlier: 8.176A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.334A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.487A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.697A pdb=" N VAL B 237 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 280 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 3.614A pdb=" N GLU B 564 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 589 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 643 Processing sheet with id=AD1, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 853 through 862 current: chain 'B' and resid 947 through 956 removed outlier: 6.533A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 962 through 972 current: chain 'L' and resid 37 through 38 Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.568A pdb=" N MET B 839 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR B 994 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N MET B 841 " --> pdb=" O TYR B 994 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.520A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.352A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 43 through 54 removed outlier: 5.734A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.551A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.695A pdb=" N LEU D 50 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.684A pdb=" N TYR E 112 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.546A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 4.200A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.652A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.551A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 103 through 105 Processing sheet with id=AF6, first strand: chain 'P' and resid 117 through 121 removed outlier: 6.069A pdb=" N LEU P 118 " --> pdb=" O TYR P 393 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE P 395 " --> pdb=" O LEU P 118 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS P 120 " --> pdb=" O PHE P 395 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA P 397 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 67 through 72 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 67 through 72 current: chain 'Q' and resid 104 through 108 removed outlier: 4.013A pdb=" N ILE Q 104 " --> pdb=" O LEU Q 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 119 through 126 current: chain 'Q' and resid 211 through 226 Processing sheet with id=AF8, first strand: chain 'S' and resid 279 through 284 Processing sheet with id=AF9, first strand: chain 'a' and resid 41 through 46 removed outlier: 6.790A pdb=" N VAL a 62 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU a 79 " --> pdb=" O VAL a 62 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP a 64 " --> pdb=" O VAL a 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL a 77 " --> pdb=" O ASP a 64 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP a 66 " --> pdb=" O GLN a 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 187 through 190 removed outlier: 6.381A pdb=" N ILE a 198 " --> pdb=" O LYS a 214 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS a 214 " --> pdb=" O ILE a 198 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE a 200 " --> pdb=" O LEU a 212 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 252 through 258 current: chain 'a' and resid 322 through 329 Processing sheet with id=AG2, first strand: chain 'a' and resid 227 through 229 Processing sheet with id=AG3, first strand: chain 'a' and resid 232 through 234 removed outlier: 3.653A pdb=" N SER a 239 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 312 through 316 Processing sheet with id=AG5, first strand: chain 'f' and resid 113 through 121 removed outlier: 3.888A pdb=" N GLN f 131 " --> pdb=" O GLU f 114 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL f 127 " --> pdb=" O SER f 118 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL f 120 " --> pdb=" O PHE f 125 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE f 125 " --> pdb=" O VAL f 120 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP f 126 " --> pdb=" O TYR f 154 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR f 154 " --> pdb=" O TRP f 126 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE f 128 " --> pdb=" O ASP f 152 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP f 152 " --> pdb=" O ILE f 128 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LYS f 130 " --> pdb=" O LEU f 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 193 through 195 Processing sheet with id=AG7, first strand: chain 'g' and resid 76 through 78 Processing sheet with id=AG8, first strand: chain 'n' and resid 269 through 272 removed outlier: 6.067A pdb=" N SER n 289 " --> pdb=" O PHE n 299 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE n 299 " --> pdb=" O SER n 289 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'n' and resid 400 through 405 removed outlier: 3.786A pdb=" N GLY n 425 " --> pdb=" O TYR n 415 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS n 426 " --> pdb=" O ASP n 443 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'n' and resid 490 through 491 Processing sheet with id=AH2, first strand: chain 'n' and resid 575 through 577 removed outlier: 4.871A pdb=" N PHE n 626 " --> pdb=" O SER n 577 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE n 655 " --> pdb=" O LEU n 670 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU n 670 " --> pdb=" O ILE n 655 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS n 657 " --> pdb=" O LYS n 668 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'n' and resid 715 through 717 removed outlier: 6.840A pdb=" N SER n 766 " --> pdb=" O LYS n 783 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS n 783 " --> pdb=" O SER n 766 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'q' and resid 321 through 326 removed outlier: 4.505A pdb=" N VAL q 321 " --> pdb=" O LYS q 338 " (cutoff:3.500A) removed outlier: 14.007A pdb=" N LYS q 333 " --> pdb=" O ASN q 359 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N ASN q 359 " --> pdb=" O LYS q 333 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU q 335 " --> pdb=" O ILE q 357 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 403 through 408 removed outlier: 6.011A pdb=" N LEU q 405 " --> pdb=" O THR q 395 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR q 395 " --> pdb=" O LEU q 405 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS q 464 " --> pdb=" O GLU q 460 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'q' and resid 574 through 578 Processing sheet with id=AH7, first strand: chain 'r' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 2 through 12 current: chain 'r' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 181 through 195 current: chain 'r' and resid 229 through 239 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 242 through 245 current: chain 't' and resid 56 through 62 WARNING: can't find start of bonding for strands! previous: chain 't' and resid 76 through 81 current: chain 't' and resid 135 through 143 removed outlier: 7.049A pdb=" N THR t 136 " --> pdb=" O LEU t 155 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU t 155 " --> pdb=" O THR t 136 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG t 138 " --> pdb=" O ILE t 153 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE t 153 " --> pdb=" O ARG t 138 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL t 140 " --> pdb=" O LEU t 151 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU t 151 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU t 142 " --> pdb=" O LYS t 149 " (cutoff:3.500A) 3065 hydrogen bonds defined for protein. 8727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.98 Time building geometry restraints manager: 14.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17264 1.33 - 1.46: 16897 1.46 - 1.59: 29578 1.59 - 1.72: 0 1.72 - 1.85: 510 Bond restraints: 64249 Sorted by residual: bond pdb=" CZ ARG a 189 " pdb=" NH2 ARG a 189 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.12e+00 bond pdb=" CZ ARG a 349 " pdb=" NH2 ARG a 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.12e+00 bond pdb=" CZ ARG a 33 " pdb=" NH2 ARG a 33 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.62e+00 bond pdb=" ND1 HIS a 536 " pdb=" CE1 HIS a 536 " ideal model delta sigma weight residual 1.321 1.346 -0.025 1.00e-02 1.00e+04 6.45e+00 bond pdb=" CD2 HIS a 173 " pdb=" NE2 HIS a 173 " ideal model delta sigma weight residual 1.374 1.402 -0.028 1.10e-02 8.26e+03 6.29e+00 ... (remaining 64244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 85381 2.49 - 4.98: 1230 4.98 - 7.47: 97 7.47 - 9.96: 13 9.96 - 12.46: 6 Bond angle restraints: 86727 Sorted by residual: angle pdb=" C GLN B 278 " pdb=" N ASP B 279 " pdb=" CA ASP B 279 " ideal model delta sigma weight residual 121.54 132.68 -11.14 1.91e+00 2.74e-01 3.40e+01 angle pdb=" CA PRO g 16 " pdb=" N PRO g 16 " pdb=" CD PRO g 16 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.14e+01 angle pdb=" C PRO a 298 " pdb=" N ILE a 299 " pdb=" CA ILE a 299 " ideal model delta sigma weight residual 120.56 127.43 -6.87 1.26e+00 6.30e-01 2.97e+01 angle pdb=" OE1 GLN a 529 " pdb=" CD GLN a 529 " pdb=" NE2 GLN a 529 " ideal model delta sigma weight residual 122.60 117.17 5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" C LYS a 22 " pdb=" N PRO a 23 " pdb=" CA PRO a 23 " ideal model delta sigma weight residual 119.56 124.79 -5.23 1.02e+00 9.61e-01 2.63e+01 ... (remaining 86722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 35566 17.66 - 35.31: 3357 35.31 - 52.97: 486 52.97 - 70.63: 85 70.63 - 88.28: 46 Dihedral angle restraints: 39540 sinusoidal: 16509 harmonic: 23031 Sorted by residual: dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual -86.00 -140.77 54.77 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CA CYS C 92 " pdb=" C CYS C 92 " pdb=" N ASP C 93 " pdb=" CA ASP C 93 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA SER a 295 " pdb=" C SER a 295 " pdb=" N SER a 296 " pdb=" CA SER a 296 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 39537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 8438 0.065 - 0.130: 1247 0.130 - 0.196: 109 0.196 - 0.261: 9 0.261 - 0.326: 2 Chirality restraints: 9805 Sorted by residual: chirality pdb=" CG LEU B 289 " pdb=" CB LEU B 289 " pdb=" CD1 LEU B 289 " pdb=" CD2 LEU B 289 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL A1015 " pdb=" CA VAL A1015 " pdb=" CG1 VAL A1015 " pdb=" CG2 VAL A1015 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CG LEU i 73 " pdb=" CB LEU i 73 " pdb=" CD1 LEU i 73 " pdb=" CD2 LEU i 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 9802 not shown) Planarity restraints: 11160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a 216 " 0.109 2.00e-02 2.50e+03 6.76e-02 9.13e+01 pdb=" CG TYR a 216 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR a 216 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR a 216 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR a 216 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR a 216 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR a 216 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR a 216 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 344 " -0.088 2.00e-02 2.50e+03 4.66e-02 5.42e+01 pdb=" CG TRP a 344 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP a 344 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP a 344 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP a 344 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP a 344 " 0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 344 " -0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP a 344 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 67 " 0.055 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR a 67 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR a 67 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR a 67 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR a 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR a 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR a 67 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR a 67 " 0.085 2.00e-02 2.50e+03 ... (remaining 11157 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 17 2.15 - 2.84: 19572 2.84 - 3.52: 87297 3.52 - 4.21: 137517 4.21 - 4.90: 245293 Nonbonded interactions: 489696 Sorted by model distance: nonbonded pdb=" CZ TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.462 3.660 nonbonded pdb=" CE1 TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.614 3.740 nonbonded pdb=" CD2 LEU a 17 " pdb=" CD2 LEU d 67 " model vdw 1.622 3.880 nonbonded pdb=" CE2 TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.664 2.992 nonbonded pdb=" CZ TYR a 21 " pdb=" NZ LYS d 71 " model vdw 1.738 2.672 ... (remaining 489691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.040 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 111.330 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3474 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 0.097 64249 Z= 0.270 Angle : 0.688 12.456 86727 Z= 0.393 Chirality : 0.046 0.326 9805 Planarity : 0.005 0.147 11160 Dihedral : 13.630 88.285 24545 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.62 (0.10), residues: 7715 helix: 1.40 (0.09), residues: 3216 sheet: 0.38 (0.15), residues: 1253 loop : -0.51 (0.11), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.004 TRP a 344 HIS 0.014 0.001 HIS a 536 PHE 0.055 0.002 PHE a 356 TYR 0.116 0.002 TYR a 216 ARG 0.011 0.001 ARG h 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1851 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1847 time to evaluate : 5.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.5932 (pm20) cc_final: 0.5730 (pm20) REVERT: A 289 ILE cc_start: 0.5385 (mt) cc_final: 0.5060 (mt) REVERT: A 426 LEU cc_start: 0.8021 (mt) cc_final: 0.7818 (mt) REVERT: A 445 ASN cc_start: 0.5850 (p0) cc_final: 0.4922 (p0) REVERT: A 454 SER cc_start: 0.7904 (t) cc_final: 0.7387 (m) REVERT: A 575 LYS cc_start: 0.7406 (mttp) cc_final: 0.6349 (mttt) REVERT: A 598 LEU cc_start: 0.7366 (tt) cc_final: 0.7071 (tp) REVERT: A 605 MET cc_start: 0.5985 (mmm) cc_final: 0.4912 (tpp) REVERT: A 608 ILE cc_start: 0.6656 (mt) cc_final: 0.6315 (mt) REVERT: A 633 VAL cc_start: 0.7306 (t) cc_final: 0.6792 (t) REVERT: A 679 ILE cc_start: 0.4879 (mm) cc_final: 0.4428 (mm) REVERT: A 701 LEU cc_start: 0.6605 (mt) cc_final: 0.6292 (mt) REVERT: A 929 LEU cc_start: 0.5705 (mt) cc_final: 0.4676 (mt) REVERT: A 1348 LEU cc_start: 0.7738 (tp) cc_final: 0.7474 (tp) REVERT: A 1349 TYR cc_start: 0.5672 (t80) cc_final: 0.5338 (t80) REVERT: A 1408 ILE cc_start: 0.7840 (mt) cc_final: 0.7446 (mt) REVERT: A 1411 GLU cc_start: 0.5602 (tt0) cc_final: 0.5298 (tt0) REVERT: A 1425 SER cc_start: 0.8207 (m) cc_final: 0.7667 (p) REVERT: B 167 ILE cc_start: 0.4376 (tt) cc_final: 0.4103 (tt) REVERT: B 359 GLU cc_start: 0.2260 (tt0) cc_final: 0.1361 (mp0) REVERT: B 446 LEU cc_start: 0.3834 (tp) cc_final: 0.3495 (mp) REVERT: B 473 MET cc_start: 0.4869 (ttt) cc_final: 0.4363 (pmm) REVERT: B 686 ASN cc_start: 0.4605 (m-40) cc_final: 0.4266 (t0) REVERT: B 747 MET cc_start: 0.3370 (mmt) cc_final: 0.2408 (mmt) REVERT: B 855 PHE cc_start: 0.2012 (t80) cc_final: 0.1274 (t80) REVERT: B 1084 GLN cc_start: 0.6190 (mp10) cc_final: 0.5737 (mp10) REVERT: B 1134 GLU cc_start: 0.7590 (mp0) cc_final: 0.6800 (mp0) REVERT: C 125 MET cc_start: 0.1212 (mtp) cc_final: 0.0940 (ptp) REVERT: C 248 ILE cc_start: 0.8558 (mt) cc_final: 0.8324 (tt) REVERT: C 252 GLN cc_start: 0.7661 (mt0) cc_final: 0.7283 (mm-40) REVERT: E 22 MET cc_start: 0.6333 (ttm) cc_final: 0.6123 (ttm) REVERT: F 94 LEU cc_start: 0.7827 (mt) cc_final: 0.7203 (mt) REVERT: F 125 LEU cc_start: 0.7616 (tp) cc_final: 0.7366 (tp) REVERT: F 128 LYS cc_start: 0.6124 (mmmt) cc_final: 0.5878 (tppt) REVERT: S 203 TYR cc_start: 0.5982 (t80) cc_final: 0.5597 (t80) REVERT: g 38 LYS cc_start: -0.3113 (tttt) cc_final: -0.3320 (pttt) REVERT: g 70 MET cc_start: -0.2885 (tpt) cc_final: -0.3408 (ttt) REVERT: g 147 LYS cc_start: 0.1824 (mttt) cc_final: 0.1589 (tptm) REVERT: i 98 LEU cc_start: 0.8283 (mt) cc_final: 0.6162 (mm) REVERT: i 110 ASP cc_start: 0.5956 (t0) cc_final: 0.5614 (t70) REVERT: j 49 MET cc_start: -0.6471 (tpt) cc_final: -0.8247 (mmt) REVERT: n 460 ILE cc_start: 0.7844 (mt) cc_final: 0.7603 (tp) REVERT: n 789 MET cc_start: 0.5524 (ppp) cc_final: 0.3542 (mtm) REVERT: q 238 MET cc_start: -0.4523 (mmp) cc_final: -0.4984 (tpt) REVERT: q 478 LEU cc_start: 0.7909 (tp) cc_final: 0.7633 (tp) REVERT: r 8 PHE cc_start: 0.5784 (m-80) cc_final: 0.5380 (m-10) REVERT: r 265 ILE cc_start: 0.8192 (mt) cc_final: 0.7737 (mt) REVERT: t 69 THR cc_start: 0.6827 (m) cc_final: 0.6277 (m) REVERT: t 105 ASP cc_start: 0.5689 (m-30) cc_final: 0.4902 (m-30) REVERT: t 200 LEU cc_start: 0.6476 (tp) cc_final: 0.5547 (tp) REVERT: u 1 MET cc_start: 0.0436 (pmm) cc_final: 0.0163 (ppp) outliers start: 4 outliers final: 2 residues processed: 1851 average time/residue: 0.6472 time to fit residues: 1942.4701 Evaluate side-chains 1109 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1107 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 651 optimal weight: 9.9990 chunk 585 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 394 optimal weight: 20.0000 chunk 312 optimal weight: 4.9990 chunk 605 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 367 optimal weight: 1.9990 chunk 450 optimal weight: 6.9990 chunk 701 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 71 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN A1059 HIS ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS B 60 GLN B 121 ASN B 215 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS B1187 ASN C 65 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 252 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN H 83 GLN Q 109 ASN S 151 GLN ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 HIS ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 GLN h 70 ASN h 165 ASN i 85 ASN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 402 HIS n 502 GLN n 622 GLN n 635 ASN ** n 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 294 GLN t 48 ASN u 9 GLN u 74 ASN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN v 60 ASN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.199877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.139014 restraints weight = 228706.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.144087 restraints weight = 176202.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.146468 restraints weight = 140291.203| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4203 r_free = 0.4203 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4203 r_free = 0.4203 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 64249 Z= 0.314 Angle : 0.756 21.024 86727 Z= 0.391 Chirality : 0.046 0.223 9805 Planarity : 0.006 0.158 11160 Dihedral : 4.790 33.370 8482 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 0.32 % Allowed : 5.19 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.40 (0.09), residues: 7715 helix: 1.00 (0.09), residues: 3299 sheet: 0.27 (0.15), residues: 1179 loop : -0.39 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 466 HIS 0.022 0.002 HIS h 45 PHE 0.040 0.003 PHE G 18 TYR 0.038 0.002 TYR A1349 ARG 0.038 0.001 ARG h 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1397 time to evaluate : 5.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9351 (p) cc_final: 0.9101 (t) REVERT: A 41 MET cc_start: 0.8753 (tmm) cc_final: 0.8310 (tmm) REVERT: A 74 MET cc_start: 0.8921 (pmm) cc_final: 0.8641 (pmm) REVERT: A 116 ASP cc_start: 0.8874 (m-30) cc_final: 0.8473 (m-30) REVERT: A 130 ASP cc_start: 0.9626 (p0) cc_final: 0.9210 (p0) REVERT: A 133 LYS cc_start: 0.8462 (mptt) cc_final: 0.8109 (mmmt) REVERT: A 225 ASN cc_start: 0.8555 (t0) cc_final: 0.8270 (t0) REVERT: A 335 ARG cc_start: 0.8966 (mmt90) cc_final: 0.8746 (ttm-80) REVERT: A 341 MET cc_start: 0.8008 (mmp) cc_final: 0.7315 (mmm) REVERT: A 348 SER cc_start: 0.6471 (m) cc_final: 0.6127 (m) REVERT: A 378 GLU cc_start: 0.9214 (tt0) cc_final: 0.8879 (tt0) REVERT: A 403 LYS cc_start: 0.9369 (tptt) cc_final: 0.9052 (tptt) REVERT: A 411 ASP cc_start: 0.9535 (m-30) cc_final: 0.9333 (m-30) REVERT: A 424 ILE cc_start: 0.8913 (mt) cc_final: 0.8416 (mt) REVERT: A 454 SER cc_start: 0.8664 (t) cc_final: 0.8426 (m) REVERT: A 455 MET cc_start: 0.8092 (ttm) cc_final: 0.7557 (ptt) REVERT: A 461 LYS cc_start: 0.7492 (tptt) cc_final: 0.7132 (mmtm) REVERT: A 478 TYR cc_start: 0.8174 (m-80) cc_final: 0.7220 (m-80) REVERT: A 486 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 487 MET cc_start: 0.8214 (mmp) cc_final: 0.7797 (mmp) REVERT: A 490 HIS cc_start: 0.9142 (m-70) cc_final: 0.8399 (m-70) REVERT: A 523 ILE cc_start: 0.9441 (mm) cc_final: 0.8606 (tt) REVERT: A 536 LEU cc_start: 0.9171 (mt) cc_final: 0.8963 (mt) REVERT: A 575 LYS cc_start: 0.8346 (mttp) cc_final: 0.7952 (mttt) REVERT: A 605 MET cc_start: 0.8386 (mmm) cc_final: 0.7705 (mmm) REVERT: A 606 LEU cc_start: 0.9546 (tp) cc_final: 0.9221 (tp) REVERT: A 614 PHE cc_start: 0.9420 (p90) cc_final: 0.9064 (p90) REVERT: A 646 PHE cc_start: 0.9836 (m-80) cc_final: 0.9272 (m-80) REVERT: A 748 MET cc_start: 0.9238 (mtm) cc_final: 0.8474 (mtm) REVERT: A 804 TYR cc_start: 0.8681 (m-80) cc_final: 0.8460 (m-80) REVERT: A 816 HIS cc_start: 0.9399 (t70) cc_final: 0.9006 (t70) REVERT: A 838 GLN cc_start: 0.9671 (tp40) cc_final: 0.9400 (tp40) REVERT: A 843 LYS cc_start: 0.9725 (mttm) cc_final: 0.9404 (mtpp) REVERT: A 935 GLN cc_start: 0.9400 (tp-100) cc_final: 0.9192 (tp-100) REVERT: A 949 ASP cc_start: 0.8239 (p0) cc_final: 0.7898 (p0) REVERT: A 1006 ILE cc_start: 0.9427 (mp) cc_final: 0.9075 (pt) REVERT: A 1063 MET cc_start: 0.8606 (mmp) cc_final: 0.8361 (mmp) REVERT: A 1074 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9298 (tm-30) REVERT: B 101 MET cc_start: 0.8914 (ppp) cc_final: 0.8397 (ppp) REVERT: B 203 PHE cc_start: 0.8339 (m-80) cc_final: 0.7959 (m-80) REVERT: B 353 LYS cc_start: 0.9317 (tttt) cc_final: 0.9098 (mtmt) REVERT: B 473 MET cc_start: 0.5741 (ttt) cc_final: 0.4890 (pmm) REVERT: B 518 HIS cc_start: 0.7198 (m90) cc_final: 0.6720 (m90) REVERT: B 519 TRP cc_start: 0.8840 (t-100) cc_final: 0.7968 (t-100) REVERT: B 635 ARG cc_start: 0.8917 (mtm180) cc_final: 0.8700 (mtm-85) REVERT: B 747 MET cc_start: 0.4123 (mmt) cc_final: 0.3482 (mmt) REVERT: B 761 HIS cc_start: 0.6352 (m-70) cc_final: 0.5867 (m-70) REVERT: B 885 MET cc_start: 0.3248 (mtt) cc_final: 0.2876 (mmm) REVERT: B 951 GLN cc_start: 0.9140 (mt0) cc_final: 0.8732 (mt0) REVERT: B 1064 TYR cc_start: 0.9365 (m-80) cc_final: 0.9094 (m-80) REVERT: B 1072 MET cc_start: 0.8421 (mtm) cc_final: 0.8088 (mtm) REVERT: B 1073 TYR cc_start: 0.9265 (m-10) cc_final: 0.9041 (m-80) REVERT: B 1082 MET cc_start: 0.1614 (mmm) cc_final: 0.1354 (mmt) REVERT: B 1135 ARG cc_start: 0.9427 (ptt90) cc_final: 0.9046 (ptt90) REVERT: B 1138 MET cc_start: 0.9587 (mmp) cc_final: 0.8859 (mmp) REVERT: B 1153 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9218 (mt-10) REVERT: B 1188 LYS cc_start: 0.8918 (mptt) cc_final: 0.8592 (mmtt) REVERT: B 1218 THR cc_start: 0.9483 (m) cc_final: 0.9234 (t) REVERT: C 1 MET cc_start: 0.7908 (tpt) cc_final: 0.7198 (tpp) REVERT: C 100 THR cc_start: 0.8042 (p) cc_final: 0.7734 (t) REVERT: C 128 ASN cc_start: 0.9726 (p0) cc_final: 0.9362 (p0) REVERT: C 252 GLN cc_start: 0.9354 (mt0) cc_final: 0.8785 (mm-40) REVERT: E 23 VAL cc_start: 0.9364 (t) cc_final: 0.8851 (t) REVERT: E 37 LEU cc_start: 0.9394 (mt) cc_final: 0.9095 (mt) REVERT: E 136 ASN cc_start: 0.7649 (t0) cc_final: 0.7002 (t0) REVERT: E 163 GLU cc_start: 0.9360 (tp30) cc_final: 0.9098 (tp30) REVERT: E 204 THR cc_start: 0.8946 (p) cc_final: 0.8743 (p) REVERT: F 89 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7492 (mm-30) REVERT: F 90 ARG cc_start: 0.8152 (ppt170) cc_final: 0.7680 (ptm-80) REVERT: F 154 ASP cc_start: 0.9294 (m-30) cc_final: 0.7690 (p0) REVERT: G 9 LEU cc_start: 0.9160 (tp) cc_final: 0.8941 (mt) REVERT: G 25 TYR cc_start: 0.8805 (m-80) cc_final: 0.8455 (m-10) REVERT: G 44 TYR cc_start: 0.8873 (m-80) cc_final: 0.8165 (m-80) REVERT: G 57 GLN cc_start: 0.9594 (pp30) cc_final: 0.9252 (pp30) REVERT: G 79 PHE cc_start: 0.9343 (t80) cc_final: 0.8970 (t80) REVERT: H 40 LEU cc_start: 0.9718 (tp) cc_final: 0.9378 (tp) REVERT: H 78 SER cc_start: 0.9271 (m) cc_final: 0.8917 (t) REVERT: H 80 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8218 (ttp80) REVERT: H 83 GLN cc_start: 0.7771 (mp10) cc_final: 0.7498 (mp10) REVERT: H 97 MET cc_start: 0.9046 (mtp) cc_final: 0.8709 (mmp) REVERT: H 116 TYR cc_start: 0.9071 (m-80) cc_final: 0.8847 (m-80) REVERT: I 1 MET cc_start: 0.6490 (tmm) cc_final: 0.6242 (tmm) REVERT: I 27 PHE cc_start: 0.8902 (m-80) cc_final: 0.8614 (m-80) REVERT: I 44 TYR cc_start: 0.8554 (t80) cc_final: 0.8186 (t80) REVERT: J 21 TYR cc_start: 0.7477 (t80) cc_final: 0.6906 (t80) REVERT: J 41 LEU cc_start: 0.8825 (mt) cc_final: 0.8573 (mt) REVERT: K 5 ASP cc_start: 0.8502 (p0) cc_final: 0.8289 (p0) REVERT: K 37 LYS cc_start: 0.8017 (mttp) cc_final: 0.7582 (mtmm) REVERT: K 53 ASP cc_start: 0.8826 (t0) cc_final: 0.8548 (t0) REVERT: K 75 ILE cc_start: 0.9101 (tp) cc_final: 0.8769 (mm) REVERT: K 85 ASP cc_start: 0.9664 (m-30) cc_final: 0.9293 (m-30) REVERT: K 98 LEU cc_start: 0.9646 (mt) cc_final: 0.9441 (mt) REVERT: M 26 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9085 (mm-30) REVERT: M 36 GLU cc_start: 0.9134 (pm20) cc_final: 0.8850 (pm20) REVERT: M 40 GLU cc_start: 0.8697 (pp20) cc_final: 0.8297 (tm-30) REVERT: M 42 ASP cc_start: 0.8474 (m-30) cc_final: 0.8241 (m-30) REVERT: P 352 MET cc_start: -0.5510 (mtm) cc_final: -0.5901 (mtt) REVERT: S 195 TYR cc_start: 0.9714 (t80) cc_final: 0.9371 (t80) REVERT: S 200 ARG cc_start: 0.9714 (ttm110) cc_final: 0.9384 (tmt170) REVERT: a 18 PHE cc_start: 0.9522 (m-80) cc_final: 0.9287 (m-80) REVERT: g 70 MET cc_start: -0.1753 (tpt) cc_final: -0.2079 (ttt) REVERT: g 147 LYS cc_start: 0.4519 (mttt) cc_final: 0.3434 (tptt) REVERT: h 50 ILE cc_start: 0.9539 (tp) cc_final: 0.9292 (tp) REVERT: j 49 MET cc_start: -0.6904 (tpt) cc_final: -0.7451 (mmt) REVERT: k 69 GLU cc_start: 0.9491 (mm-30) cc_final: 0.8950 (mt-10) REVERT: n 469 ASP cc_start: 0.9726 (t0) cc_final: 0.9479 (m-30) REVERT: n 637 TYR cc_start: 0.9457 (m-80) cc_final: 0.9055 (m-80) REVERT: n 789 MET cc_start: 0.3877 (ppp) cc_final: 0.3311 (mtm) REVERT: q 238 MET cc_start: -0.1678 (mmp) cc_final: -0.2574 (tpt) REVERT: r 81 MET cc_start: 0.7246 (pmm) cc_final: 0.6904 (pmm) REVERT: r 214 GLN cc_start: 0.9484 (pm20) cc_final: 0.9167 (pm20) REVERT: r 215 TYR cc_start: 0.8985 (p90) cc_final: 0.8317 (p90) REVERT: r 235 ILE cc_start: 0.9640 (mt) cc_final: 0.9413 (mt) REVERT: r 276 MET cc_start: 0.8251 (ppp) cc_final: 0.8031 (ppp) REVERT: t 47 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8896 (mmtm) REVERT: t 65 HIS cc_start: 0.8038 (m90) cc_final: 0.7811 (m-70) REVERT: t 78 MET cc_start: 0.9422 (ttp) cc_final: 0.8938 (ttp) REVERT: t 93 PHE cc_start: 0.7135 (m-80) cc_final: 0.6608 (m-80) REVERT: t 141 ASN cc_start: 0.9054 (p0) cc_final: 0.8848 (p0) REVERT: t 195 ASN cc_start: 0.8582 (t0) cc_final: 0.8184 (t0) REVERT: u 1 MET cc_start: 0.7725 (pmm) cc_final: 0.6535 (ppp) REVERT: v 4 GLN cc_start: 0.9782 (tp40) cc_final: 0.9524 (tm-30) REVERT: w 121 MET cc_start: -0.5905 (mmp) cc_final: -0.6236 (mmt) outliers start: 23 outliers final: 7 residues processed: 1416 average time/residue: 0.6377 time to fit residues: 1496.4859 Evaluate side-chains 1068 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1061 time to evaluate : 5.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 421 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 627 optimal weight: 20.0000 chunk 753 optimal weight: 10.0000 chunk 387 optimal weight: 0.8980 chunk 344 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 763 optimal weight: 9.9990 chunk 389 optimal weight: 3.9990 chunk 268 optimal weight: 0.1980 chunk 212 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 811 GLN ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 494 HIS B 513 GLN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN H 133 ASN H 139 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN S 191 ASN S 257 GLN a 106 ASN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 529 GLN ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 201 HIS ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN ** i 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 51 HIS k 93 GLN ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 701 ASN ** n 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 294 GLN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN v 61 GLN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 86 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.197945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.136747 restraints weight = 234096.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.142335 restraints weight = 175980.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.145209 restraints weight = 134379.267| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4194 r_free = 0.4194 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4194 r_free = 0.4194 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 64249 Z= 0.242 Angle : 0.636 11.263 86727 Z= 0.333 Chirality : 0.044 0.293 9805 Planarity : 0.005 0.086 11160 Dihedral : 4.640 30.370 8482 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Rotamer: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.58 (0.09), residues: 7715 helix: 1.18 (0.09), residues: 3308 sheet: 0.22 (0.15), residues: 1190 loop : -0.27 (0.11), residues: 3217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP q 279 HIS 0.014 0.001 HIS E 146 PHE 0.043 0.002 PHE i 70 TYR 0.038 0.002 TYR A1349 ARG 0.016 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1349 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.9426 (m-10) cc_final: 0.9167 (m-10) REVERT: A 57 ARG cc_start: 0.9159 (mtm180) cc_final: 0.8818 (mtm-85) REVERT: A 74 MET cc_start: 0.8815 (pmm) cc_final: 0.8448 (pmm) REVERT: A 116 ASP cc_start: 0.8910 (m-30) cc_final: 0.8488 (m-30) REVERT: A 133 LYS cc_start: 0.8419 (mptt) cc_final: 0.8123 (mmmt) REVERT: A 207 ILE cc_start: 0.9655 (mt) cc_final: 0.9365 (mt) REVERT: A 225 ASN cc_start: 0.8682 (t0) cc_final: 0.8450 (t0) REVERT: A 348 SER cc_start: 0.5997 (m) cc_final: 0.4755 (m) REVERT: A 378 GLU cc_start: 0.9175 (tt0) cc_final: 0.8867 (tt0) REVERT: A 411 ASP cc_start: 0.9662 (m-30) cc_final: 0.9405 (p0) REVERT: A 414 ASP cc_start: 0.8876 (t0) cc_final: 0.8312 (t0) REVERT: A 417 TYR cc_start: 0.9083 (m-80) cc_final: 0.8673 (m-80) REVERT: A 424 ILE cc_start: 0.8778 (mt) cc_final: 0.8526 (mt) REVERT: A 436 ILE cc_start: 0.9251 (pt) cc_final: 0.8993 (pt) REVERT: A 437 MET cc_start: 0.7823 (mmp) cc_final: 0.7588 (mmm) REVERT: A 454 SER cc_start: 0.8758 (t) cc_final: 0.8518 (m) REVERT: A 455 MET cc_start: 0.7851 (ttm) cc_final: 0.7285 (ttm) REVERT: A 478 TYR cc_start: 0.7959 (m-80) cc_final: 0.7556 (m-80) REVERT: A 486 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 487 MET cc_start: 0.8393 (mmp) cc_final: 0.8052 (mmp) REVERT: A 490 HIS cc_start: 0.8987 (m-70) cc_final: 0.8195 (m-70) REVERT: A 523 ILE cc_start: 0.9363 (mm) cc_final: 0.8498 (tt) REVERT: A 531 ILE cc_start: 0.9345 (tt) cc_final: 0.9099 (tt) REVERT: A 606 LEU cc_start: 0.9528 (tp) cc_final: 0.9223 (tp) REVERT: A 609 ASP cc_start: 0.9586 (m-30) cc_final: 0.9340 (p0) REVERT: A 614 PHE cc_start: 0.9464 (p90) cc_final: 0.8860 (p90) REVERT: A 646 PHE cc_start: 0.9817 (m-80) cc_final: 0.9311 (m-80) REVERT: A 679 ILE cc_start: 0.7845 (mm) cc_final: 0.7633 (mm) REVERT: A 692 ASP cc_start: 0.9359 (m-30) cc_final: 0.9097 (m-30) REVERT: A 748 MET cc_start: 0.9227 (mtm) cc_final: 0.8837 (mtp) REVERT: A 816 HIS cc_start: 0.9340 (t70) cc_final: 0.8972 (t70) REVERT: A 830 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8332 (mtpt) REVERT: A 838 GLN cc_start: 0.9642 (tp40) cc_final: 0.9372 (tp40) REVERT: A 843 LYS cc_start: 0.9757 (mttm) cc_final: 0.9435 (mtpp) REVERT: A 866 PHE cc_start: 0.9129 (m-10) cc_final: 0.8437 (m-10) REVERT: A 913 LEU cc_start: 0.9268 (tp) cc_final: 0.8932 (tp) REVERT: A 932 GLU cc_start: 0.8586 (pt0) cc_final: 0.8323 (pt0) REVERT: A 935 GLN cc_start: 0.9447 (tp-100) cc_final: 0.9015 (tp-100) REVERT: A 942 PHE cc_start: 0.9453 (m-10) cc_final: 0.9241 (m-10) REVERT: A 1006 ILE cc_start: 0.9176 (mp) cc_final: 0.8949 (pt) REVERT: A 1063 MET cc_start: 0.8577 (mmp) cc_final: 0.8084 (mmt) REVERT: A 1074 GLU cc_start: 0.9491 (tm-30) cc_final: 0.9238 (tm-30) REVERT: A 1280 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8458 (tm-30) REVERT: A 1348 LEU cc_start: 0.9662 (tp) cc_final: 0.9397 (tp) REVERT: A 1398 MET cc_start: 0.9542 (ttp) cc_final: 0.9301 (ttp) REVERT: A 1402 PHE cc_start: 0.8551 (p90) cc_final: 0.8286 (p90) REVERT: A 1430 LEU cc_start: 0.9536 (mt) cc_final: 0.9327 (mt) REVERT: B 101 MET cc_start: 0.8948 (ppp) cc_final: 0.8266 (ppp) REVERT: B 173 MET cc_start: 0.8493 (ttp) cc_final: 0.8269 (ttp) REVERT: B 275 TYR cc_start: 0.8943 (m-80) cc_final: 0.8684 (m-80) REVERT: B 313 MET cc_start: 0.8164 (mpp) cc_final: 0.6585 (ptt) REVERT: B 386 LEU cc_start: 0.6119 (mp) cc_final: 0.5610 (mt) REVERT: B 390 LEU cc_start: 0.8382 (mt) cc_final: 0.8038 (mt) REVERT: B 473 MET cc_start: 0.5389 (ttt) cc_final: 0.4777 (pmm) REVERT: B 514 LEU cc_start: 0.8581 (tp) cc_final: 0.7750 (tp) REVERT: B 518 HIS cc_start: 0.7165 (m90) cc_final: 0.6559 (m-70) REVERT: B 635 ARG cc_start: 0.8923 (mtm180) cc_final: 0.8673 (mtp180) REVERT: B 747 MET cc_start: 0.4350 (mmt) cc_final: 0.3806 (mmt) REVERT: B 773 MET cc_start: 0.3047 (mmp) cc_final: 0.2807 (mmt) REVERT: B 873 THR cc_start: 0.9289 (p) cc_final: 0.9024 (p) REVERT: B 931 TYR cc_start: 0.9004 (m-80) cc_final: 0.8645 (p90) REVERT: B 951 GLN cc_start: 0.9125 (mt0) cc_final: 0.8685 (mt0) REVERT: B 1064 TYR cc_start: 0.9283 (m-80) cc_final: 0.9082 (m-80) REVERT: B 1072 MET cc_start: 0.8280 (mtm) cc_final: 0.7875 (mtm) REVERT: B 1073 TYR cc_start: 0.9302 (m-10) cc_final: 0.9010 (m-80) REVERT: B 1111 MET cc_start: 0.6974 (pmm) cc_final: 0.6729 (mpp) REVERT: B 1135 ARG cc_start: 0.9417 (ptt90) cc_final: 0.9081 (ptt90) REVERT: B 1136 ASP cc_start: 0.9618 (m-30) cc_final: 0.9120 (m-30) REVERT: B 1138 MET cc_start: 0.9579 (mmp) cc_final: 0.9318 (mmp) REVERT: B 1153 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9165 (mt-10) REVERT: B 1188 LYS cc_start: 0.8815 (mptt) cc_final: 0.8597 (mmtt) REVERT: B 1218 THR cc_start: 0.9366 (m) cc_final: 0.9052 (t) REVERT: C 1 MET cc_start: 0.7930 (tpt) cc_final: 0.7073 (tpt) REVERT: C 75 MET cc_start: 0.8873 (mpp) cc_final: 0.8524 (mpp) REVERT: C 100 THR cc_start: 0.8067 (p) cc_final: 0.7748 (t) REVERT: C 128 ASN cc_start: 0.9719 (p0) cc_final: 0.9365 (p0) REVERT: C 190 ASP cc_start: 0.9051 (t0) cc_final: 0.8267 (m-30) REVERT: C 252 GLN cc_start: 0.9607 (tt0) cc_final: 0.9112 (mm110) REVERT: E 34 GLU cc_start: 0.9763 (pt0) cc_final: 0.9430 (pt0) REVERT: E 37 LEU cc_start: 0.9416 (mt) cc_final: 0.9126 (mt) REVERT: E 57 MET cc_start: 0.5846 (ptt) cc_final: 0.5604 (ptt) REVERT: E 121 MET cc_start: 0.9442 (pmm) cc_final: 0.9156 (pmm) REVERT: E 163 GLU cc_start: 0.9282 (tp30) cc_final: 0.9019 (tp30) REVERT: E 177 ARG cc_start: 0.8403 (tmm160) cc_final: 0.7915 (ttt-90) REVERT: F 85 MET cc_start: 0.9064 (ptm) cc_final: 0.8856 (ppp) REVERT: F 89 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7762 (mm-30) REVERT: F 94 LEU cc_start: 0.9115 (mt) cc_final: 0.8876 (mt) REVERT: F 151 LEU cc_start: 0.8659 (mt) cc_final: 0.8445 (mt) REVERT: G 9 LEU cc_start: 0.9296 (tp) cc_final: 0.9085 (mt) REVERT: G 57 GLN cc_start: 0.9622 (pp30) cc_final: 0.9328 (pp30) REVERT: H 38 LEU cc_start: 0.9673 (tp) cc_final: 0.9426 (tp) REVERT: H 41 ASP cc_start: 0.9380 (m-30) cc_final: 0.9037 (m-30) REVERT: H 96 VAL cc_start: 0.7724 (t) cc_final: 0.7234 (t) REVERT: I 1 MET cc_start: 0.6740 (tmm) cc_final: 0.6148 (tmm) REVERT: I 27 PHE cc_start: 0.9084 (m-80) cc_final: 0.8867 (m-80) REVERT: I 44 TYR cc_start: 0.8605 (t80) cc_final: 0.8200 (t80) REVERT: I 97 MET cc_start: 0.8929 (mmt) cc_final: 0.8600 (mmt) REVERT: J 21 TYR cc_start: 0.7399 (t80) cc_final: 0.6791 (t80) REVERT: J 41 LEU cc_start: 0.9100 (mt) cc_final: 0.8778 (mt) REVERT: K 33 ILE cc_start: 0.9648 (tp) cc_final: 0.9428 (tp) REVERT: K 53 ASP cc_start: 0.8710 (t0) cc_final: 0.8358 (t0) REVERT: K 62 LYS cc_start: 0.7565 (pttt) cc_final: 0.7085 (pttt) REVERT: M 26 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9051 (mm-30) REVERT: M 36 GLU cc_start: 0.9243 (pm20) cc_final: 0.8713 (pp20) REVERT: M 38 PHE cc_start: 0.8693 (p90) cc_final: 0.8378 (p90) REVERT: M 40 GLU cc_start: 0.8504 (pp20) cc_final: 0.8053 (tm-30) REVERT: P 132 ASP cc_start: 0.5546 (t0) cc_final: 0.4969 (t0) REVERT: S 195 TYR cc_start: 0.9622 (t80) cc_final: 0.9284 (t80) REVERT: a 529 GLN cc_start: 0.5706 (tp-100) cc_final: 0.5446 (tm-30) REVERT: d 81 PHE cc_start: 0.9120 (t80) cc_final: 0.8885 (t80) REVERT: g 70 MET cc_start: -0.0989 (tpt) cc_final: -0.1687 (ttt) REVERT: g 147 LYS cc_start: 0.3941 (mttt) cc_final: 0.3171 (tptt) REVERT: h 163 PHE cc_start: 0.8917 (m-10) cc_final: 0.8714 (m-80) REVERT: j 49 MET cc_start: -0.6941 (tpt) cc_final: -0.7586 (mmt) REVERT: k 55 PHE cc_start: 0.6371 (t80) cc_final: 0.6016 (t80) REVERT: k 59 LEU cc_start: 0.9610 (tp) cc_final: 0.9390 (mt) REVERT: k 69 GLU cc_start: 0.9479 (mm-30) cc_final: 0.8980 (mt-10) REVERT: n 469 ASP cc_start: 0.9732 (t0) cc_final: 0.9503 (m-30) REVERT: n 637 TYR cc_start: 0.9467 (m-80) cc_final: 0.9068 (m-80) REVERT: n 789 MET cc_start: 0.3804 (ppp) cc_final: 0.3292 (mtm) REVERT: q 207 MET cc_start: 0.8087 (ppp) cc_final: 0.7379 (tmm) REVERT: q 238 MET cc_start: -0.1518 (mmp) cc_final: -0.2552 (tpt) REVERT: q 411 MET cc_start: 0.8974 (pmm) cc_final: 0.8356 (mmt) REVERT: r 81 MET cc_start: 0.7728 (pmm) cc_final: 0.7380 (pmm) REVERT: r 214 GLN cc_start: 0.9417 (pm20) cc_final: 0.8777 (pp30) REVERT: r 233 GLN cc_start: 0.7985 (tp40) cc_final: 0.7764 (tp40) REVERT: r 265 ILE cc_start: 0.9645 (mm) cc_final: 0.9322 (mm) REVERT: r 276 MET cc_start: 0.8309 (ppp) cc_final: 0.8063 (ppp) REVERT: r 299 ARG cc_start: 0.8370 (mtt180) cc_final: 0.8105 (mtp180) REVERT: s 68 ILE cc_start: 0.3014 (pt) cc_final: 0.2792 (pt) REVERT: t 32 ARG cc_start: 0.6824 (mtp85) cc_final: 0.6187 (mmt-90) REVERT: t 40 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7404 (ttm110) REVERT: t 47 LYS cc_start: 0.9204 (mmtm) cc_final: 0.8932 (mmtm) REVERT: t 57 MET cc_start: 0.9145 (ttp) cc_final: 0.8846 (ttp) REVERT: t 65 HIS cc_start: 0.8320 (m90) cc_final: 0.7874 (m90) REVERT: t 78 MET cc_start: 0.9435 (ttp) cc_final: 0.9063 (ttp) REVERT: t 93 PHE cc_start: 0.7209 (m-80) cc_final: 0.6733 (m-80) REVERT: t 102 GLU cc_start: 0.9352 (tt0) cc_final: 0.9146 (tt0) REVERT: t 105 ASP cc_start: 0.9265 (m-30) cc_final: 0.9019 (m-30) REVERT: t 141 ASN cc_start: 0.9009 (p0) cc_final: 0.8607 (p0) REVERT: t 195 ASN cc_start: 0.8538 (t0) cc_final: 0.8193 (t0) REVERT: u 1 MET cc_start: 0.8014 (pmm) cc_final: 0.7219 (ppp) REVERT: v 41 PHE cc_start: 0.7611 (p90) cc_final: 0.6999 (t80) REVERT: w 121 MET cc_start: -0.5749 (mmp) cc_final: -0.6119 (mmt) outliers start: 13 outliers final: 1 residues processed: 1359 average time/residue: 0.6413 time to fit residues: 1442.9396 Evaluate side-chains 1058 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1057 time to evaluate : 5.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 266 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 477 optimal weight: 8.9990 chunk 708 optimal weight: 10.0000 chunk 397 optimal weight: 0.6980 chunk 261 optimal weight: 0.4980 chunk 661 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 528 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 54 ASN A 394 ASN A 435 HIS A 439 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 GLN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS B 363 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 494 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS B1161 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 GLN a 30 ASN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN h 151 GLN h 165 ASN k 14 ASN ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 383 HIS ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 303 GLN q 528 HIS r 226 HIS ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 245 GLN r 269 ASN r 294 GLN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.194234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.133640 restraints weight = 236878.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.138552 restraints weight = 179871.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.141188 restraints weight = 140438.070| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 64249 Z= 0.234 Angle : 0.640 11.779 86727 Z= 0.335 Chirality : 0.044 0.210 9805 Planarity : 0.005 0.136 11160 Dihedral : 4.655 27.333 8482 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.10), residues: 7715 helix: 1.09 (0.09), residues: 3328 sheet: 0.02 (0.15), residues: 1213 loop : -0.26 (0.11), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP q 279 HIS 0.020 0.001 HIS q 306 PHE 0.047 0.002 PHE G 18 TYR 0.038 0.002 TYR A1349 ARG 0.015 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1327 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9029 (tp) cc_final: 0.8700 (mt) REVERT: A 74 MET cc_start: 0.8736 (pmm) cc_final: 0.8374 (pmm) REVERT: A 116 ASP cc_start: 0.8895 (m-30) cc_final: 0.8478 (m-30) REVERT: A 207 ILE cc_start: 0.9699 (mt) cc_final: 0.9469 (mt) REVERT: A 346 ASP cc_start: 0.8616 (p0) cc_final: 0.8238 (p0) REVERT: A 348 SER cc_start: 0.5726 (m) cc_final: 0.5399 (t) REVERT: A 361 LEU cc_start: 0.9514 (tp) cc_final: 0.9293 (tp) REVERT: A 375 THR cc_start: 0.8329 (p) cc_final: 0.7576 (p) REVERT: A 411 ASP cc_start: 0.9619 (m-30) cc_final: 0.9306 (p0) REVERT: A 424 ILE cc_start: 0.8892 (mt) cc_final: 0.8578 (mt) REVERT: A 436 ILE cc_start: 0.9221 (pt) cc_final: 0.8961 (pt) REVERT: A 437 MET cc_start: 0.7927 (mmp) cc_final: 0.7651 (mmm) REVERT: A 444 PHE cc_start: 0.8365 (t80) cc_final: 0.7728 (t80) REVERT: A 455 MET cc_start: 0.7563 (ttm) cc_final: 0.6936 (ttm) REVERT: A 486 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 487 MET cc_start: 0.8303 (mmp) cc_final: 0.7674 (mmp) REVERT: A 490 HIS cc_start: 0.8923 (m-70) cc_final: 0.8368 (m-70) REVERT: A 523 ILE cc_start: 0.9342 (mm) cc_final: 0.8974 (mm) REVERT: A 606 LEU cc_start: 0.9629 (tp) cc_final: 0.9393 (tp) REVERT: A 609 ASP cc_start: 0.9619 (m-30) cc_final: 0.9371 (p0) REVERT: A 614 PHE cc_start: 0.9402 (p90) cc_final: 0.8703 (p90) REVERT: A 646 PHE cc_start: 0.9796 (m-80) cc_final: 0.9446 (m-80) REVERT: A 679 ILE cc_start: 0.7815 (mm) cc_final: 0.7581 (mm) REVERT: A 687 LYS cc_start: 0.9476 (pttm) cc_final: 0.9258 (pttt) REVERT: A 705 LYS cc_start: 0.9174 (mmpt) cc_final: 0.8915 (mmmt) REVERT: A 742 ASN cc_start: 0.9046 (m110) cc_final: 0.8759 (m110) REVERT: A 748 MET cc_start: 0.9200 (mtm) cc_final: 0.8805 (mtm) REVERT: A 816 HIS cc_start: 0.9382 (t70) cc_final: 0.9082 (t70) REVERT: A 838 GLN cc_start: 0.9703 (tp40) cc_final: 0.9419 (tp40) REVERT: A 843 LYS cc_start: 0.9770 (mttm) cc_final: 0.9417 (mtpp) REVERT: A 866 PHE cc_start: 0.8631 (m-10) cc_final: 0.8286 (m-10) REVERT: A 913 LEU cc_start: 0.9326 (tp) cc_final: 0.8888 (tp) REVERT: A 932 GLU cc_start: 0.8714 (pt0) cc_final: 0.8306 (pt0) REVERT: A 935 GLN cc_start: 0.9414 (tp-100) cc_final: 0.9108 (tp-100) REVERT: A 942 PHE cc_start: 0.9453 (m-10) cc_final: 0.9239 (m-10) REVERT: A 949 ASP cc_start: 0.8439 (p0) cc_final: 0.8148 (p0) REVERT: A 981 LEU cc_start: 0.8299 (pp) cc_final: 0.6772 (mt) REVERT: A 1006 ILE cc_start: 0.9499 (mp) cc_final: 0.9137 (pt) REVERT: A 1063 MET cc_start: 0.8675 (mmp) cc_final: 0.8099 (mmt) REVERT: A 1074 GLU cc_start: 0.9541 (tm-30) cc_final: 0.9327 (tm-30) REVERT: A 1174 PHE cc_start: 0.7633 (m-80) cc_final: 0.7331 (m-80) REVERT: A 1280 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 1289 ARG cc_start: 0.8970 (ptp90) cc_final: 0.8444 (ptp-170) REVERT: A 1348 LEU cc_start: 0.9762 (tp) cc_final: 0.9512 (tp) REVERT: A 1398 MET cc_start: 0.9580 (ttp) cc_final: 0.9310 (ttp) REVERT: A 1402 PHE cc_start: 0.8538 (p90) cc_final: 0.8255 (p90) REVERT: B 313 MET cc_start: 0.8494 (mpp) cc_final: 0.7231 (ptt) REVERT: B 386 LEU cc_start: 0.6004 (mp) cc_final: 0.5543 (mp) REVERT: B 390 LEU cc_start: 0.8472 (mt) cc_final: 0.8137 (mt) REVERT: B 473 MET cc_start: 0.5433 (ttt) cc_final: 0.4782 (pmm) REVERT: B 514 LEU cc_start: 0.8571 (tp) cc_final: 0.7522 (tp) REVERT: B 515 HIS cc_start: 0.6059 (t-90) cc_final: 0.5106 (t70) REVERT: B 518 HIS cc_start: 0.7492 (m90) cc_final: 0.6629 (m-70) REVERT: B 739 THR cc_start: 0.9297 (p) cc_final: 0.9033 (p) REVERT: B 747 MET cc_start: 0.4984 (mmt) cc_final: 0.4536 (mmt) REVERT: B 931 TYR cc_start: 0.9015 (m-80) cc_final: 0.8653 (p90) REVERT: B 951 GLN cc_start: 0.9135 (mt0) cc_final: 0.8826 (mt0) REVERT: B 979 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8836 (ttmt) REVERT: B 1064 TYR cc_start: 0.9324 (m-80) cc_final: 0.9099 (m-80) REVERT: B 1072 MET cc_start: 0.8270 (mtm) cc_final: 0.7977 (mtm) REVERT: B 1073 TYR cc_start: 0.9320 (m-10) cc_final: 0.9098 (m-80) REVERT: B 1082 MET cc_start: 0.1864 (mmm) cc_final: 0.1141 (mmm) REVERT: B 1111 MET cc_start: 0.6875 (pmm) cc_final: 0.6510 (pmm) REVERT: B 1136 ASP cc_start: 0.9628 (m-30) cc_final: 0.9149 (m-30) REVERT: B 1138 MET cc_start: 0.9628 (mmp) cc_final: 0.9386 (mmp) REVERT: B 1153 GLU cc_start: 0.9369 (mt-10) cc_final: 0.9118 (mt-10) REVERT: B 1188 LYS cc_start: 0.8767 (mptt) cc_final: 0.8535 (mmtm) REVERT: B 1218 THR cc_start: 0.9396 (m) cc_final: 0.9087 (t) REVERT: C 1 MET cc_start: 0.8065 (tpt) cc_final: 0.5983 (tmm) REVERT: C 9 LYS cc_start: 0.9280 (mptt) cc_final: 0.9046 (mmtm) REVERT: C 75 MET cc_start: 0.9018 (mpp) cc_final: 0.8768 (mpp) REVERT: C 100 THR cc_start: 0.8112 (p) cc_final: 0.7846 (t) REVERT: C 128 ASN cc_start: 0.9761 (p0) cc_final: 0.9394 (p0) REVERT: C 192 TRP cc_start: 0.6737 (t60) cc_final: 0.6505 (t60) REVERT: C 252 GLN cc_start: 0.9651 (tt0) cc_final: 0.9066 (mm-40) REVERT: E 34 GLU cc_start: 0.9578 (pt0) cc_final: 0.9310 (pt0) REVERT: E 37 LEU cc_start: 0.9412 (mt) cc_final: 0.9159 (mt) REVERT: E 57 MET cc_start: 0.6020 (ptt) cc_final: 0.5817 (ptt) REVERT: E 121 MET cc_start: 0.9479 (pmm) cc_final: 0.9200 (pmm) REVERT: E 163 GLU cc_start: 0.9371 (tp30) cc_final: 0.9097 (tp30) REVERT: F 85 MET cc_start: 0.9309 (ptm) cc_final: 0.8682 (ptm) REVERT: F 89 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7882 (mm-30) REVERT: G 9 LEU cc_start: 0.9366 (tp) cc_final: 0.9055 (mt) REVERT: G 44 TYR cc_start: 0.8919 (m-80) cc_final: 0.8148 (m-80) REVERT: G 57 GLN cc_start: 0.9656 (pp30) cc_final: 0.9338 (pp30) REVERT: G 79 PHE cc_start: 0.9331 (t80) cc_final: 0.8918 (t80) REVERT: H 41 ASP cc_start: 0.9268 (m-30) cc_final: 0.8973 (m-30) REVERT: H 116 TYR cc_start: 0.9452 (m-80) cc_final: 0.9026 (m-80) REVERT: H 117 SER cc_start: 0.9260 (t) cc_final: 0.9034 (m) REVERT: I 1 MET cc_start: 0.6800 (tmm) cc_final: 0.6306 (tmm) REVERT: I 27 PHE cc_start: 0.9118 (m-80) cc_final: 0.8845 (m-80) REVERT: I 44 TYR cc_start: 0.8646 (t80) cc_final: 0.8217 (t80) REVERT: I 86 PHE cc_start: 0.8990 (p90) cc_final: 0.8678 (p90) REVERT: I 89 GLN cc_start: 0.5375 (pp30) cc_final: 0.5145 (pp30) REVERT: I 94 ASP cc_start: 0.8880 (t0) cc_final: 0.8595 (m-30) REVERT: I 97 MET cc_start: 0.8908 (mmt) cc_final: 0.8697 (mmt) REVERT: J 21 TYR cc_start: 0.7532 (t80) cc_final: 0.6917 (t80) REVERT: J 41 LEU cc_start: 0.9296 (mt) cc_final: 0.9027 (mt) REVERT: K 73 LEU cc_start: 0.9191 (tp) cc_final: 0.8970 (tp) REVERT: K 98 LEU cc_start: 0.9658 (mt) cc_final: 0.9389 (mt) REVERT: L 53 HIS cc_start: 0.9040 (t70) cc_final: 0.8779 (t70) REVERT: L 55 ILE cc_start: 0.8974 (mt) cc_final: 0.8733 (mt) REVERT: M 26 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9068 (mm-30) REVERT: M 36 GLU cc_start: 0.9254 (pm20) cc_final: 0.8790 (tm-30) REVERT: P 132 ASP cc_start: 0.5342 (t0) cc_final: 0.4982 (t0) REVERT: S 195 TYR cc_start: 0.9663 (t80) cc_final: 0.9413 (t80) REVERT: a 529 GLN cc_start: 0.5774 (tp-100) cc_final: 0.5446 (tm-30) REVERT: g 70 MET cc_start: -0.0890 (tpt) cc_final: -0.1756 (ttt) REVERT: g 147 LYS cc_start: 0.4213 (mttt) cc_final: 0.3602 (tptt) REVERT: g 151 ILE cc_start: 0.0919 (mt) cc_final: 0.0413 (mt) REVERT: j 49 MET cc_start: -0.6786 (tpt) cc_final: -0.7524 (mmt) REVERT: n 386 PHE cc_start: 0.8790 (m-80) cc_final: 0.8536 (m-80) REVERT: n 469 ASP cc_start: 0.9742 (t0) cc_final: 0.9513 (m-30) REVERT: n 637 TYR cc_start: 0.9408 (m-80) cc_final: 0.8886 (m-80) REVERT: n 789 MET cc_start: 0.3811 (ppp) cc_final: 0.3304 (mtm) REVERT: q 207 MET cc_start: 0.7627 (ppp) cc_final: 0.7286 (tmm) REVERT: q 238 MET cc_start: -0.0884 (mmp) cc_final: -0.1441 (tpt) REVERT: q 411 MET cc_start: 0.8968 (pmm) cc_final: 0.8489 (mmm) REVERT: r 32 LEU cc_start: 0.9355 (mp) cc_final: 0.8877 (mp) REVERT: r 34 TYR cc_start: 0.8265 (p90) cc_final: 0.7951 (p90) REVERT: r 74 TYR cc_start: 0.8026 (m-10) cc_final: 0.7688 (m-80) REVERT: r 81 MET cc_start: 0.7884 (pmm) cc_final: 0.7301 (pmm) REVERT: r 105 THR cc_start: 0.9494 (p) cc_final: 0.9279 (p) REVERT: r 214 GLN cc_start: 0.9426 (pm20) cc_final: 0.8688 (pp30) REVERT: r 221 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8858 (ttpp) REVERT: r 272 GLU cc_start: 0.9248 (mp0) cc_final: 0.8974 (mp0) REVERT: r 276 MET cc_start: 0.8314 (ppp) cc_final: 0.8059 (ppp) REVERT: r 299 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8173 (mtp180) REVERT: t 21 LYS cc_start: 0.9262 (ptpp) cc_final: 0.9002 (pttm) REVERT: t 40 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7292 (ttm110) REVERT: t 57 MET cc_start: 0.9187 (ttp) cc_final: 0.8913 (ttp) REVERT: t 65 HIS cc_start: 0.7964 (m90) cc_final: 0.7700 (m-70) REVERT: t 93 PHE cc_start: 0.7458 (m-10) cc_final: 0.6950 (m-80) REVERT: t 105 ASP cc_start: 0.9290 (m-30) cc_final: 0.9028 (m-30) REVERT: t 141 ASN cc_start: 0.9247 (p0) cc_final: 0.8607 (p0) REVERT: t 151 LEU cc_start: 0.9666 (tt) cc_final: 0.9181 (mp) REVERT: t 152 LEU cc_start: 0.9747 (tp) cc_final: 0.9539 (tp) REVERT: t 195 ASN cc_start: 0.8580 (t0) cc_final: 0.8221 (t0) REVERT: u 1 MET cc_start: 0.7794 (pmm) cc_final: 0.6783 (ppp) REVERT: u 127 GLU cc_start: 0.9087 (pt0) cc_final: 0.8871 (pp20) REVERT: v 8 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8497 (mt-10) REVERT: v 41 PHE cc_start: 0.7607 (p90) cc_final: 0.6987 (t80) REVERT: w 121 MET cc_start: -0.5687 (mmp) cc_final: -0.6096 (mmt) outliers start: 3 outliers final: 1 residues processed: 1328 average time/residue: 0.6313 time to fit residues: 1393.1783 Evaluate side-chains 1066 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1065 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 12 optimal weight: 5.9990 chunk 551 optimal weight: 0.0470 chunk 178 optimal weight: 3.9990 chunk 399 optimal weight: 0.7980 chunk 480 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 318 optimal weight: 10.0000 chunk 734 optimal weight: 7.9990 chunk 682 optimal weight: 2.9990 chunk 297 optimal weight: 6.9990 chunk 544 optimal weight: 7.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 969 GLN A1008 GLN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1393 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 494 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN H 133 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 GLN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 75 GLN h 150 GLN h 151 GLN ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 51 HIS ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 444 GLN ** r 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 245 GLN r 269 ASN r 294 GLN ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN v 68 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.192651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.134394 restraints weight = 238026.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.139913 restraints weight = 178884.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.141870 restraints weight = 141344.305| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 64249 Z= 0.215 Angle : 0.626 10.612 86727 Z= 0.326 Chirality : 0.044 0.344 9805 Planarity : 0.005 0.110 11160 Dihedral : 4.653 36.205 8482 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.51 (0.10), residues: 7715 helix: 1.14 (0.09), residues: 3320 sheet: 0.02 (0.15), residues: 1190 loop : -0.28 (0.11), residues: 3205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP q 279 HIS 0.010 0.001 HIS A1173 PHE 0.043 0.002 PHE G 18 TYR 0.035 0.002 TYR f 100 ARG 0.016 0.001 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1311 time to evaluate : 5.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9027 (tp) cc_final: 0.8695 (mt) REVERT: A 74 MET cc_start: 0.8600 (pmm) cc_final: 0.8076 (pmm) REVERT: A 108 MET cc_start: 0.7735 (ppp) cc_final: 0.7410 (ppp) REVERT: A 207 ILE cc_start: 0.9678 (mt) cc_final: 0.9401 (mt) REVERT: A 225 ASN cc_start: 0.8743 (t0) cc_final: 0.8483 (t0) REVERT: A 346 ASP cc_start: 0.8540 (p0) cc_final: 0.8187 (p0) REVERT: A 348 SER cc_start: 0.6024 (m) cc_final: 0.5684 (t) REVERT: A 375 THR cc_start: 0.8670 (p) cc_final: 0.8307 (t) REVERT: A 411 ASP cc_start: 0.9547 (m-30) cc_final: 0.9017 (m-30) REVERT: A 414 ASP cc_start: 0.8747 (t0) cc_final: 0.8440 (t0) REVERT: A 437 MET cc_start: 0.7967 (mmp) cc_final: 0.7622 (mmm) REVERT: A 444 PHE cc_start: 0.8424 (t80) cc_final: 0.7886 (t80) REVERT: A 455 MET cc_start: 0.7428 (ttm) cc_final: 0.6978 (ttm) REVERT: A 468 PHE cc_start: 0.8063 (m-80) cc_final: 0.7557 (m-80) REVERT: A 486 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 487 MET cc_start: 0.8386 (mmp) cc_final: 0.7640 (mmp) REVERT: A 490 HIS cc_start: 0.8892 (m-70) cc_final: 0.8355 (m-70) REVERT: A 523 ILE cc_start: 0.9319 (mm) cc_final: 0.8957 (mm) REVERT: A 603 ASN cc_start: 0.9098 (m-40) cc_final: 0.8689 (m-40) REVERT: A 606 LEU cc_start: 0.9658 (tp) cc_final: 0.9456 (tp) REVERT: A 614 PHE cc_start: 0.9353 (p90) cc_final: 0.8616 (p90) REVERT: A 646 PHE cc_start: 0.9720 (m-80) cc_final: 0.9450 (m-80) REVERT: A 679 ILE cc_start: 0.7718 (mm) cc_final: 0.7497 (mm) REVERT: A 687 LYS cc_start: 0.9462 (pttm) cc_final: 0.9226 (pttt) REVERT: A 705 LYS cc_start: 0.9197 (mmpt) cc_final: 0.8858 (mmmt) REVERT: A 748 MET cc_start: 0.9248 (mtm) cc_final: 0.8616 (mtm) REVERT: A 804 TYR cc_start: 0.9225 (m-80) cc_final: 0.8628 (m-80) REVERT: A 816 HIS cc_start: 0.9336 (t70) cc_final: 0.9127 (t70) REVERT: A 830 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7938 (mtpt) REVERT: A 838 GLN cc_start: 0.9728 (tp40) cc_final: 0.9471 (tp40) REVERT: A 843 LYS cc_start: 0.9668 (mttm) cc_final: 0.8914 (mtpp) REVERT: A 866 PHE cc_start: 0.8556 (m-10) cc_final: 0.8175 (m-10) REVERT: A 913 LEU cc_start: 0.9319 (tp) cc_final: 0.8864 (tp) REVERT: A 935 GLN cc_start: 0.9469 (tp-100) cc_final: 0.9166 (tp-100) REVERT: A 942 PHE cc_start: 0.9405 (m-10) cc_final: 0.9202 (m-10) REVERT: A 949 ASP cc_start: 0.8370 (p0) cc_final: 0.7874 (p0) REVERT: A 981 LEU cc_start: 0.8467 (pp) cc_final: 0.7060 (mt) REVERT: A 995 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9074 (mt-10) REVERT: A 1063 MET cc_start: 0.8619 (mmt) cc_final: 0.8230 (mmt) REVERT: A 1074 GLU cc_start: 0.9490 (tm-30) cc_final: 0.9237 (tm-30) REVERT: A 1155 ASP cc_start: 0.7549 (t0) cc_final: 0.7266 (t0) REVERT: A 1174 PHE cc_start: 0.8015 (m-80) cc_final: 0.7710 (m-80) REVERT: A 1209 MET cc_start: 0.6525 (tpp) cc_final: 0.6051 (tpp) REVERT: A 1280 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 1285 MET cc_start: 0.6417 (mmt) cc_final: 0.5897 (mmt) REVERT: A 1398 MET cc_start: 0.9571 (ttp) cc_final: 0.9178 (ttp) REVERT: A 1402 PHE cc_start: 0.8427 (p90) cc_final: 0.8166 (p90) REVERT: A 1442 ASP cc_start: 0.9113 (m-30) cc_final: 0.8634 (p0) REVERT: B 173 MET cc_start: 0.8468 (ttp) cc_final: 0.8079 (ttp) REVERT: B 432 MET cc_start: 0.7644 (ptt) cc_final: 0.7442 (ptt) REVERT: B 473 MET cc_start: 0.5120 (ttt) cc_final: 0.4382 (pmm) REVERT: B 514 LEU cc_start: 0.8547 (tp) cc_final: 0.8191 (tp) REVERT: B 518 HIS cc_start: 0.7700 (m90) cc_final: 0.6990 (m-70) REVERT: B 601 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7472 (mmt-90) REVERT: B 635 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8595 (mtp180) REVERT: B 747 MET cc_start: 0.5452 (mmt) cc_final: 0.5025 (mmt) REVERT: B 931 TYR cc_start: 0.8994 (m-80) cc_final: 0.8640 (p90) REVERT: B 951 GLN cc_start: 0.8889 (mt0) cc_final: 0.8528 (mt0) REVERT: B 979 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8803 (ttmt) REVERT: B 1064 TYR cc_start: 0.9285 (m-80) cc_final: 0.8986 (m-80) REVERT: B 1072 MET cc_start: 0.8334 (mtm) cc_final: 0.7970 (mtm) REVERT: B 1073 TYR cc_start: 0.9273 (m-10) cc_final: 0.9034 (m-80) REVERT: B 1082 MET cc_start: 0.1679 (mmm) cc_final: 0.1061 (mmm) REVERT: B 1111 MET cc_start: 0.6792 (pmm) cc_final: 0.6552 (pmm) REVERT: B 1134 GLU cc_start: 0.8656 (mp0) cc_final: 0.7807 (mp0) REVERT: B 1138 MET cc_start: 0.9614 (mmp) cc_final: 0.9372 (mmp) REVERT: B 1153 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9133 (mt-10) REVERT: B 1188 LYS cc_start: 0.8765 (mptt) cc_final: 0.8533 (mmtm) REVERT: B 1218 THR cc_start: 0.9324 (m) cc_final: 0.9055 (t) REVERT: C 1 MET cc_start: 0.8063 (tpt) cc_final: 0.7346 (tpp) REVERT: C 9 LYS cc_start: 0.9350 (mptt) cc_final: 0.9094 (mmtm) REVERT: C 21 ILE cc_start: 0.9480 (tt) cc_final: 0.8898 (tt) REVERT: C 75 MET cc_start: 0.8996 (mpp) cc_final: 0.8298 (mpp) REVERT: C 82 TYR cc_start: 0.7081 (m-10) cc_final: 0.6854 (m-80) REVERT: C 100 THR cc_start: 0.8417 (p) cc_final: 0.8120 (t) REVERT: C 128 ASN cc_start: 0.9733 (p0) cc_final: 0.9473 (p0) REVERT: C 246 ARG cc_start: 0.9420 (mtt180) cc_final: 0.8648 (mtt180) REVERT: C 252 GLN cc_start: 0.9660 (tt0) cc_final: 0.9159 (mm-40) REVERT: E 28 TYR cc_start: 0.7313 (m-80) cc_final: 0.6601 (m-10) REVERT: E 34 GLU cc_start: 0.9728 (pt0) cc_final: 0.9462 (pt0) REVERT: E 121 MET cc_start: 0.9416 (pmm) cc_final: 0.9070 (pmm) REVERT: E 163 GLU cc_start: 0.9329 (tp30) cc_final: 0.9063 (tp30) REVERT: E 174 GLN cc_start: 0.8900 (mp10) cc_final: 0.8693 (mp10) REVERT: E 201 LYS cc_start: 0.8323 (tmmt) cc_final: 0.7993 (mptt) REVERT: F 151 LEU cc_start: 0.8344 (mt) cc_final: 0.7955 (mt) REVERT: G 44 TYR cc_start: 0.8993 (m-80) cc_final: 0.8219 (m-80) REVERT: G 57 GLN cc_start: 0.9416 (pp30) cc_final: 0.9061 (pp30) REVERT: G 70 PHE cc_start: 0.9525 (m-10) cc_final: 0.9149 (m-80) REVERT: G 79 PHE cc_start: 0.9370 (t80) cc_final: 0.8850 (t80) REVERT: H 38 LEU cc_start: 0.9736 (tp) cc_final: 0.9502 (tp) REVERT: H 41 ASP cc_start: 0.9275 (m-30) cc_final: 0.9012 (m-30) REVERT: H 78 SER cc_start: 0.9310 (m) cc_final: 0.8858 (t) REVERT: H 117 SER cc_start: 0.9234 (t) cc_final: 0.9004 (m) REVERT: I 1 MET cc_start: 0.6535 (tmm) cc_final: 0.6008 (tmm) REVERT: I 44 TYR cc_start: 0.8667 (t80) cc_final: 0.8159 (t80) REVERT: I 86 PHE cc_start: 0.8928 (p90) cc_final: 0.8539 (p90) REVERT: I 94 ASP cc_start: 0.8882 (t0) cc_final: 0.8512 (m-30) REVERT: I 97 MET cc_start: 0.8877 (mmt) cc_final: 0.8557 (mmt) REVERT: J 21 TYR cc_start: 0.7457 (t80) cc_final: 0.7108 (t80) REVERT: K 39 ASP cc_start: 0.8838 (p0) cc_final: 0.8636 (p0) REVERT: K 49 GLU cc_start: 0.8898 (tp30) cc_final: 0.8606 (tm-30) REVERT: K 53 ASP cc_start: 0.9042 (t0) cc_final: 0.8787 (t70) REVERT: K 73 LEU cc_start: 0.9140 (tp) cc_final: 0.8847 (tp) REVERT: K 75 ILE cc_start: 0.8955 (mm) cc_final: 0.8726 (mm) REVERT: K 98 LEU cc_start: 0.9688 (mt) cc_final: 0.9341 (mt) REVERT: L 29 TYR cc_start: 0.7874 (m-10) cc_final: 0.7469 (m-80) REVERT: L 53 HIS cc_start: 0.9119 (t70) cc_final: 0.8808 (t70) REVERT: M 36 GLU cc_start: 0.9243 (pm20) cc_final: 0.9003 (pm20) REVERT: M 40 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8315 (tm-30) REVERT: M 42 ASP cc_start: 0.8393 (m-30) cc_final: 0.7935 (m-30) REVERT: P 132 ASP cc_start: 0.5261 (t0) cc_final: 0.4735 (t0) REVERT: S 192 GLU cc_start: 0.9159 (tp30) cc_final: 0.8902 (tp30) REVERT: S 195 TYR cc_start: 0.9642 (t80) cc_final: 0.9264 (t80) REVERT: a 529 GLN cc_start: 0.5818 (tp-100) cc_final: 0.5501 (tm-30) REVERT: d 81 PHE cc_start: 0.9253 (t80) cc_final: 0.9043 (t80) REVERT: f 99 MET cc_start: 0.6188 (ptt) cc_final: 0.5492 (ppp) REVERT: g 70 MET cc_start: -0.0349 (tpt) cc_final: -0.0596 (ttt) REVERT: h 48 ARG cc_start: 0.8979 (pmt-80) cc_final: 0.8641 (pmt-80) REVERT: j 49 MET cc_start: -0.6739 (tpt) cc_final: -0.7429 (mmt) REVERT: n 386 PHE cc_start: 0.8885 (m-80) cc_final: 0.8597 (m-80) REVERT: n 469 ASP cc_start: 0.9744 (t0) cc_final: 0.9522 (m-30) REVERT: n 637 TYR cc_start: 0.9371 (m-80) cc_final: 0.8847 (m-80) REVERT: n 789 MET cc_start: 0.4117 (ppp) cc_final: 0.3604 (mtm) REVERT: q 207 MET cc_start: 0.8026 (ppp) cc_final: 0.7445 (tmm) REVERT: q 238 MET cc_start: -0.1459 (mmp) cc_final: -0.1970 (tpt) REVERT: q 411 MET cc_start: 0.8829 (pmm) cc_final: 0.8483 (mmm) REVERT: r 32 LEU cc_start: 0.9378 (mp) cc_final: 0.8979 (mp) REVERT: r 34 TYR cc_start: 0.8313 (p90) cc_final: 0.7957 (p90) REVERT: r 74 TYR cc_start: 0.8114 (m-10) cc_final: 0.7857 (m-80) REVERT: r 81 MET cc_start: 0.8070 (pmm) cc_final: 0.7585 (pmm) REVERT: r 214 GLN cc_start: 0.9376 (pm20) cc_final: 0.8676 (pp30) REVERT: r 215 TYR cc_start: 0.9345 (p90) cc_final: 0.9116 (p90) REVERT: r 216 LEU cc_start: 0.9549 (tt) cc_final: 0.9317 (pp) REVERT: r 218 ILE cc_start: 0.9502 (mt) cc_final: 0.9278 (mt) REVERT: r 221 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8678 (ttpp) REVERT: r 276 MET cc_start: 0.8233 (ppp) cc_final: 0.7965 (ppp) REVERT: r 299 ARG cc_start: 0.8571 (mtt180) cc_final: 0.8311 (mtp180) REVERT: t 21 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8908 (ptpp) REVERT: t 29 LEU cc_start: 0.7873 (tt) cc_final: 0.7484 (mt) REVERT: t 40 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7747 (ttm110) REVERT: t 57 MET cc_start: 0.9225 (ttp) cc_final: 0.8560 (ttp) REVERT: t 78 MET cc_start: 0.9267 (ttm) cc_final: 0.8912 (ttm) REVERT: t 93 PHE cc_start: 0.7570 (m-10) cc_final: 0.7050 (m-80) REVERT: t 105 ASP cc_start: 0.9321 (m-30) cc_final: 0.9028 (m-30) REVERT: t 141 ASN cc_start: 0.9110 (p0) cc_final: 0.8882 (p0) REVERT: t 151 LEU cc_start: 0.9602 (tt) cc_final: 0.9068 (mt) REVERT: t 152 LEU cc_start: 0.9758 (tp) cc_final: 0.9550 (tp) REVERT: t 195 ASN cc_start: 0.8530 (t0) cc_final: 0.8159 (t0) REVERT: u 1 MET cc_start: 0.8223 (pmm) cc_final: 0.7342 (ppp) REVERT: v 8 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8603 (mt-10) REVERT: v 41 PHE cc_start: 0.7671 (p90) cc_final: 0.7050 (t80) REVERT: w 121 MET cc_start: -0.5217 (mmp) cc_final: -0.5633 (mmt) outliers start: 3 outliers final: 1 residues processed: 1314 average time/residue: 0.6336 time to fit residues: 1380.2752 Evaluate side-chains 1066 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1065 time to evaluate : 5.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 366 optimal weight: 0.9990 chunk 709 optimal weight: 0.0570 chunk 628 optimal weight: 30.0000 chunk 645 optimal weight: 20.0000 chunk 292 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS ** A1378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1161 HIS C 31 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 151 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN I 12 ASN J 23 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 ASN a 118 HIS a 177 GLN a 562 GLN ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 ASN ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN h 151 GLN h 165 ASN i 82 ASN ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 399 ASN n 701 ASN ** n 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 269 ASN r 294 GLN ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN v 61 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.190573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.132697 restraints weight = 238699.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.137947 restraints weight = 181618.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.139436 restraints weight = 139428.841| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 64249 Z= 0.219 Angle : 0.640 12.754 86727 Z= 0.333 Chirality : 0.044 0.232 9805 Planarity : 0.005 0.103 11160 Dihedral : 4.674 35.690 8482 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 7715 helix: 1.12 (0.09), residues: 3314 sheet: -0.03 (0.15), residues: 1194 loop : -0.30 (0.11), residues: 3207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP q 279 HIS 0.008 0.001 HIS n 116 PHE 0.074 0.002 PHE G 18 TYR 0.032 0.002 TYR B1198 ARG 0.012 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1327 time to evaluate : 5.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8658 (pmm) cc_final: 0.8031 (pmm) REVERT: A 207 ILE cc_start: 0.9702 (mt) cc_final: 0.9489 (pt) REVERT: A 225 ASN cc_start: 0.8839 (t0) cc_final: 0.8576 (t0) REVERT: A 335 ARG cc_start: 0.8962 (ttp-170) cc_final: 0.8582 (ttm-80) REVERT: A 346 ASP cc_start: 0.8492 (p0) cc_final: 0.7832 (p0) REVERT: A 411 ASP cc_start: 0.9501 (m-30) cc_final: 0.8907 (m-30) REVERT: A 436 ILE cc_start: 0.9366 (pt) cc_final: 0.9135 (pt) REVERT: A 437 MET cc_start: 0.8045 (mmp) cc_final: 0.7674 (mmm) REVERT: A 444 PHE cc_start: 0.8392 (t80) cc_final: 0.7607 (t80) REVERT: A 455 MET cc_start: 0.7451 (ttm) cc_final: 0.6996 (ttm) REVERT: A 468 PHE cc_start: 0.8080 (m-80) cc_final: 0.7630 (m-80) REVERT: A 478 TYR cc_start: 0.7991 (m-80) cc_final: 0.7024 (m-80) REVERT: A 486 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 487 MET cc_start: 0.8374 (mmp) cc_final: 0.7543 (mmp) REVERT: A 490 HIS cc_start: 0.8929 (m-70) cc_final: 0.8156 (m-70) REVERT: A 509 LEU cc_start: 0.9039 (mm) cc_final: 0.8762 (mp) REVERT: A 523 ILE cc_start: 0.9323 (mm) cc_final: 0.9003 (mm) REVERT: A 548 ASN cc_start: 0.9682 (m-40) cc_final: 0.9426 (m-40) REVERT: A 590 ARG cc_start: 0.8012 (tmm160) cc_final: 0.7707 (tmm-80) REVERT: A 603 ASN cc_start: 0.9044 (m-40) cc_final: 0.8672 (m-40) REVERT: A 605 MET cc_start: 0.9420 (tpt) cc_final: 0.9019 (tpp) REVERT: A 614 PHE cc_start: 0.9370 (p90) cc_final: 0.8589 (p90) REVERT: A 646 PHE cc_start: 0.9659 (m-80) cc_final: 0.9367 (m-80) REVERT: A 748 MET cc_start: 0.9129 (mtm) cc_final: 0.8563 (mtm) REVERT: A 804 TYR cc_start: 0.9340 (m-80) cc_final: 0.8747 (m-80) REVERT: A 830 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7984 (mtpt) REVERT: A 838 GLN cc_start: 0.9726 (tp40) cc_final: 0.9446 (tp40) REVERT: A 843 LYS cc_start: 0.9647 (mttm) cc_final: 0.8808 (mtpp) REVERT: A 866 PHE cc_start: 0.8480 (m-10) cc_final: 0.8128 (m-10) REVERT: A 913 LEU cc_start: 0.9340 (tp) cc_final: 0.9004 (tp) REVERT: A 935 GLN cc_start: 0.9470 (tp-100) cc_final: 0.9174 (tp-100) REVERT: A 949 ASP cc_start: 0.8386 (p0) cc_final: 0.7974 (p0) REVERT: A 995 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9078 (mt-10) REVERT: A 1063 MET cc_start: 0.8587 (mmt) cc_final: 0.8281 (mmt) REVERT: A 1074 GLU cc_start: 0.9483 (tm-30) cc_final: 0.9222 (tm-30) REVERT: A 1155 ASP cc_start: 0.7909 (t0) cc_final: 0.7644 (t0) REVERT: A 1174 PHE cc_start: 0.8256 (m-80) cc_final: 0.7848 (m-80) REVERT: A 1348 LEU cc_start: 0.9781 (tp) cc_final: 0.9558 (tp) REVERT: A 1402 PHE cc_start: 0.8386 (p90) cc_final: 0.8076 (p90) REVERT: B 169 ARG cc_start: 0.8703 (ttm-80) cc_final: 0.8432 (ttt90) REVERT: B 173 MET cc_start: 0.8647 (ttp) cc_final: 0.8415 (ttp) REVERT: B 392 ARG cc_start: 0.8965 (tpm170) cc_final: 0.8640 (mmm160) REVERT: B 473 MET cc_start: 0.4977 (ttt) cc_final: 0.4351 (pmm) REVERT: B 515 HIS cc_start: 0.5520 (t-90) cc_final: 0.5007 (t70) REVERT: B 518 HIS cc_start: 0.6993 (m90) cc_final: 0.6006 (m90) REVERT: B 635 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8628 (mtp180) REVERT: B 739 THR cc_start: 0.9316 (p) cc_final: 0.9071 (p) REVERT: B 747 MET cc_start: 0.5861 (mmt) cc_final: 0.5520 (mmt) REVERT: B 931 TYR cc_start: 0.8972 (m-80) cc_final: 0.8597 (p90) REVERT: B 951 GLN cc_start: 0.8934 (mt0) cc_final: 0.8665 (mt0) REVERT: B 1064 TYR cc_start: 0.9275 (m-80) cc_final: 0.8961 (m-80) REVERT: B 1072 MET cc_start: 0.8246 (mtm) cc_final: 0.7852 (mtm) REVERT: B 1073 TYR cc_start: 0.9337 (m-10) cc_final: 0.9133 (m-80) REVERT: B 1082 MET cc_start: 0.2422 (mmm) cc_final: 0.1747 (mmt) REVERT: B 1091 TYR cc_start: 0.6964 (t80) cc_final: 0.6367 (t80) REVERT: B 1111 MET cc_start: 0.6945 (pmm) cc_final: 0.6649 (pmm) REVERT: B 1134 GLU cc_start: 0.8641 (mp0) cc_final: 0.7999 (mp0) REVERT: B 1135 ARG cc_start: 0.9131 (pmt-80) cc_final: 0.8614 (pmt-80) REVERT: B 1136 ASP cc_start: 0.9379 (m-30) cc_final: 0.8998 (m-30) REVERT: B 1138 MET cc_start: 0.9599 (mmp) cc_final: 0.9360 (mmp) REVERT: B 1153 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9078 (mt-10) REVERT: B 1188 LYS cc_start: 0.8761 (mptt) cc_final: 0.8289 (mmtm) REVERT: B 1218 THR cc_start: 0.9305 (m) cc_final: 0.9064 (t) REVERT: C 1 MET cc_start: 0.8134 (tpt) cc_final: 0.7230 (tpp) REVERT: C 75 MET cc_start: 0.9044 (mpp) cc_final: 0.8815 (mpp) REVERT: C 114 TYR cc_start: 0.7694 (m-10) cc_final: 0.7352 (m-10) REVERT: C 157 CYS cc_start: 0.6307 (t) cc_final: 0.5728 (t) REVERT: C 190 ASP cc_start: 0.9051 (t70) cc_final: 0.8365 (m-30) REVERT: C 209 TYR cc_start: 0.8329 (m-80) cc_final: 0.8050 (m-80) REVERT: C 226 ASP cc_start: 0.9480 (m-30) cc_final: 0.9070 (t70) REVERT: C 230 MET cc_start: 0.2958 (mmp) cc_final: 0.2700 (mmm) REVERT: C 252 GLN cc_start: 0.9667 (tt0) cc_final: 0.9174 (mm-40) REVERT: E 17 ARG cc_start: 0.8439 (mmp80) cc_final: 0.8010 (tpp-160) REVERT: E 28 TYR cc_start: 0.7522 (m-80) cc_final: 0.6933 (m-10) REVERT: E 34 GLU cc_start: 0.9694 (pt0) cc_final: 0.9486 (pt0) REVERT: E 112 TYR cc_start: 0.8923 (p90) cc_final: 0.8697 (p90) REVERT: E 121 MET cc_start: 0.9496 (pmm) cc_final: 0.9182 (pmm) REVERT: E 163 GLU cc_start: 0.9353 (tp30) cc_final: 0.9093 (tp30) REVERT: E 201 LYS cc_start: 0.8546 (tmmt) cc_final: 0.8172 (mptt) REVERT: F 85 MET cc_start: 0.9384 (ppp) cc_final: 0.9091 (ppp) REVERT: F 108 PHE cc_start: 0.7674 (m-80) cc_final: 0.7116 (m-80) REVERT: F 110 ASP cc_start: 0.9535 (p0) cc_final: 0.9325 (p0) REVERT: F 137 TYR cc_start: 0.7978 (m-80) cc_final: 0.7350 (m-80) REVERT: F 149 GLU cc_start: 0.9123 (tp30) cc_final: 0.8797 (mm-30) REVERT: G 9 LEU cc_start: 0.9554 (mt) cc_final: 0.9353 (mt) REVERT: G 17 PHE cc_start: 0.9744 (m-80) cc_final: 0.9528 (m-80) REVERT: G 44 TYR cc_start: 0.9293 (m-80) cc_final: 0.8949 (m-80) REVERT: G 57 GLN cc_start: 0.9463 (pp30) cc_final: 0.9142 (pp30) REVERT: G 70 PHE cc_start: 0.9571 (m-10) cc_final: 0.9330 (m-80) REVERT: G 79 PHE cc_start: 0.9338 (t80) cc_final: 0.8898 (t80) REVERT: H 38 LEU cc_start: 0.9767 (tp) cc_final: 0.9561 (tp) REVERT: H 41 ASP cc_start: 0.9232 (m-30) cc_final: 0.8925 (m-30) REVERT: H 78 SER cc_start: 0.9318 (m) cc_final: 0.8878 (t) REVERT: H 117 SER cc_start: 0.9057 (t) cc_final: 0.8636 (m) REVERT: I 1 MET cc_start: 0.6732 (tmm) cc_final: 0.6243 (tmm) REVERT: I 27 PHE cc_start: 0.9242 (m-80) cc_final: 0.8974 (m-80) REVERT: I 44 TYR cc_start: 0.8665 (t80) cc_final: 0.8170 (t80) REVERT: I 55 THR cc_start: 0.7049 (p) cc_final: 0.6783 (p) REVERT: I 86 PHE cc_start: 0.8807 (p90) cc_final: 0.8434 (p90) REVERT: I 89 GLN cc_start: 0.5477 (pp30) cc_final: 0.5170 (pp30) REVERT: J 21 TYR cc_start: 0.7618 (t80) cc_final: 0.7081 (t80) REVERT: K 39 ASP cc_start: 0.8954 (p0) cc_final: 0.8635 (p0) REVERT: K 49 GLU cc_start: 0.8951 (tp30) cc_final: 0.8422 (tm-30) REVERT: K 53 ASP cc_start: 0.9127 (t0) cc_final: 0.8872 (t0) REVERT: K 73 LEU cc_start: 0.9083 (tp) cc_final: 0.8840 (tp) REVERT: K 75 ILE cc_start: 0.9015 (mm) cc_final: 0.8769 (mm) REVERT: K 98 LEU cc_start: 0.9724 (mt) cc_final: 0.9298 (mt) REVERT: L 29 TYR cc_start: 0.7989 (m-10) cc_final: 0.7500 (m-80) REVERT: L 55 ILE cc_start: 0.8995 (mt) cc_final: 0.8776 (mt) REVERT: M 36 GLU cc_start: 0.9279 (pm20) cc_final: 0.9022 (pm20) REVERT: M 40 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8243 (tm-30) REVERT: M 42 ASP cc_start: 0.8165 (m-30) cc_final: 0.7640 (m-30) REVERT: P 132 ASP cc_start: 0.5399 (t0) cc_final: 0.5071 (t0) REVERT: S 195 TYR cc_start: 0.9627 (t80) cc_final: 0.9341 (t80) REVERT: a 529 GLN cc_start: 0.5731 (tp-100) cc_final: 0.5399 (tm-30) REVERT: d 81 PHE cc_start: 0.9314 (t80) cc_final: 0.9094 (t80) REVERT: f 99 MET cc_start: 0.6048 (ptt) cc_final: 0.5430 (ppp) REVERT: g 70 MET cc_start: -0.0447 (tpt) cc_final: -0.0926 (ttt) REVERT: h 48 ARG cc_start: 0.9030 (pmt-80) cc_final: 0.8818 (pmt-80) REVERT: i 99 LYS cc_start: 0.9656 (mmpt) cc_final: 0.9348 (mttt) REVERT: j 49 MET cc_start: -0.6758 (tpt) cc_final: -0.7340 (mmt) REVERT: k 51 HIS cc_start: 0.9193 (t70) cc_final: 0.8865 (t70) REVERT: k 72 LEU cc_start: 0.9688 (mt) cc_final: 0.9354 (tp) REVERT: n 386 PHE cc_start: 0.8939 (m-80) cc_final: 0.8620 (m-80) REVERT: n 469 ASP cc_start: 0.9743 (t0) cc_final: 0.9526 (m-30) REVERT: n 637 TYR cc_start: 0.9401 (m-80) cc_final: 0.8891 (m-80) REVERT: n 789 MET cc_start: 0.4145 (ppp) cc_final: 0.3680 (mtm) REVERT: q 207 MET cc_start: 0.8175 (ppp) cc_final: 0.7617 (tmm) REVERT: q 238 MET cc_start: -0.1457 (mmp) cc_final: -0.1979 (tpt) REVERT: q 284 LEU cc_start: 0.9055 (tp) cc_final: 0.8829 (tp) REVERT: q 411 MET cc_start: 0.8889 (pmm) cc_final: 0.8276 (mpp) REVERT: r 32 LEU cc_start: 0.9375 (mp) cc_final: 0.8955 (mp) REVERT: r 34 TYR cc_start: 0.8337 (p90) cc_final: 0.7928 (p90) REVERT: r 74 TYR cc_start: 0.8403 (m-10) cc_final: 0.7967 (m-80) REVERT: r 81 MET cc_start: 0.7690 (pmm) cc_final: 0.7373 (pmm) REVERT: r 214 GLN cc_start: 0.9421 (pm20) cc_final: 0.9109 (pm20) REVERT: r 215 TYR cc_start: 0.8765 (p90) cc_final: 0.8339 (p90) REVERT: r 216 LEU cc_start: 0.9640 (tt) cc_final: 0.9424 (tt) REVERT: r 221 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8565 (ttpp) REVERT: r 261 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7665 (tmm-80) REVERT: r 276 MET cc_start: 0.8253 (ppp) cc_final: 0.7982 (ppp) REVERT: r 299 ARG cc_start: 0.8546 (mtt180) cc_final: 0.7872 (tpt-90) REVERT: s 68 ILE cc_start: 0.1390 (mm) cc_final: 0.0909 (mm) REVERT: t 21 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8954 (ptpp) REVERT: t 29 LEU cc_start: 0.7974 (tt) cc_final: 0.7618 (mt) REVERT: t 56 LEU cc_start: 0.9107 (mp) cc_final: 0.8887 (tt) REVERT: t 65 HIS cc_start: 0.8152 (m-70) cc_final: 0.7889 (m-70) REVERT: t 78 MET cc_start: 0.9182 (ttm) cc_final: 0.8905 (ttm) REVERT: t 93 PHE cc_start: 0.7687 (m-10) cc_final: 0.7160 (m-80) REVERT: t 141 ASN cc_start: 0.9147 (p0) cc_final: 0.8932 (p0) REVERT: t 151 LEU cc_start: 0.9512 (tt) cc_final: 0.8959 (mp) REVERT: t 152 LEU cc_start: 0.9759 (tp) cc_final: 0.9539 (tp) REVERT: t 195 ASN cc_start: 0.8417 (t0) cc_final: 0.8012 (t0) REVERT: u 1 MET cc_start: 0.8428 (pmm) cc_final: 0.7591 (ppp) REVERT: v 8 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8827 (mt-10) REVERT: v 41 PHE cc_start: 0.7795 (p90) cc_final: 0.7226 (t80) REVERT: w 121 MET cc_start: -0.5028 (mmp) cc_final: -0.5409 (mmt) outliers start: 0 outliers final: 0 residues processed: 1327 average time/residue: 0.6238 time to fit residues: 1378.7502 Evaluate side-chains 1066 residues out of total 7103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1066 time to evaluate : 5.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6675 > 50: distance: 105 - 107: 18.178 distance: 107 - 108: 9.210 distance: 108 - 109: 24.723 distance: 108 - 111: 31.068 distance: 109 - 110: 3.588 distance: 109 - 113: 32.318 distance: 111 - 112: 44.303 distance: 113 - 114: 18.372 distance: 113 - 119: 40.939 distance: 114 - 115: 13.509 distance: 114 - 117: 12.388 distance: 115 - 120: 15.078 distance: 117 - 118: 32.919 distance: 118 - 119: 25.164 distance: 120 - 121: 36.031 distance: 121 - 122: 23.576 distance: 121 - 124: 16.422 distance: 122 - 123: 34.622 distance: 122 - 128: 24.644 distance: 124 - 125: 18.895 distance: 125 - 126: 30.762 distance: 125 - 127: 9.405 distance: 128 - 129: 7.442 distance: 129 - 130: 43.461 distance: 129 - 132: 11.996 distance: 130 - 131: 5.664 distance: 130 - 135: 49.283 distance: 132 - 133: 22.539 distance: 132 - 134: 40.551 distance: 135 - 136: 48.016 distance: 136 - 137: 19.036 distance: 136 - 139: 31.431 distance: 137 - 138: 49.274 distance: 137 - 147: 50.063 distance: 139 - 140: 31.247 distance: 140 - 141: 45.646 distance: 140 - 142: 33.082 distance: 141 - 143: 4.261 distance: 142 - 144: 47.623 distance: 143 - 145: 38.809 distance: 144 - 145: 20.438 distance: 145 - 146: 20.097 distance: 147 - 148: 20.229 distance: 148 - 149: 23.900 distance: 148 - 151: 34.843 distance: 149 - 150: 48.620 distance: 149 - 158: 29.471 distance: 151 - 152: 43.729 distance: 152 - 153: 16.572 distance: 153 - 154: 7.371 distance: 154 - 155: 19.498 distance: 155 - 156: 28.690 distance: 155 - 157: 13.438 distance: 158 - 159: 40.878 distance: 159 - 160: 41.741 distance: 159 - 162: 30.949 distance: 160 - 161: 34.959 distance: 160 - 168: 43.022 distance: 162 - 163: 30.139 distance: 163 - 164: 27.355 distance: 163 - 165: 40.374 distance: 164 - 166: 25.224 distance: 165 - 167: 5.882 distance: 166 - 167: 16.045 distance: 168 - 169: 25.374 distance: 169 - 170: 38.448 distance: 169 - 172: 36.465 distance: 170 - 171: 35.357 distance: 170 - 177: 4.291 distance: 172 - 173: 44.200 distance: 173 - 174: 20.422 distance: 174 - 175: 15.631 distance: 174 - 176: 29.454 distance: 177 - 178: 41.313 distance: 178 - 179: 27.038 distance: 178 - 181: 36.334 distance: 179 - 180: 45.308 distance: 179 - 185: 39.675 distance: 181 - 182: 13.966 distance: 182 - 183: 11.534 distance: 182 - 184: 46.630 distance: 185 - 186: 18.094 distance: 186 - 187: 10.565 distance: 186 - 189: 9.025 distance: 187 - 188: 22.015 distance: 187 - 193: 22.058 distance: 189 - 190: 34.273 distance: 189 - 191: 25.615 distance: 190 - 192: 3.341