Starting phenix.real_space_refine on Tue Aug 26 06:54:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g8n_51133/08_2025/9g8n_51133.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g8n_51133/08_2025/9g8n_51133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g8n_51133/08_2025/9g8n_51133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g8n_51133/08_2025/9g8n_51133.map" model { file = "/net/cci-nas-00/data/ceres_data/9g8n_51133/08_2025/9g8n_51133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g8n_51133/08_2025/9g8n_51133.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Anisotropic ADP refinement not supported. Converting 48 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 197 5.16 5 C 21491 2.51 5 N 6040 2.21 5 O 6633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34405 Number of models: 1 Model: "" Number of chains: 13 Chain: "L" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1819 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 233} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain: "O" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1566 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "F" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2194 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "H" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "J" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1414 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "X" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 841 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 16, 'rna3p_pyr': 28} Link IDs: {'rna2p': 16, 'rna3p': 27} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U%rna3p_pyr:plan': 4, ' C%rna2p_pyr:plan': 1, ' C%rna2p_pyr:plan2': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 7438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7438 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 47, 'TRANS': 901} Chain breaks: 1 Chain: "G" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1852 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 18, 'TRANS': 232} Chain breaks: 1 Chain: "I" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2263 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Chain: "E" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 525 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain breaks: 2 Chain: "K" Number of atoms: 2764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2764 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 15, 'TRANS': 337} Chain: "M" Number of atoms: 7903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7903 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 42, 'TRANS': 932} Chain breaks: 4 Time building chain proxies: 6.63, per 1000 atoms: 0.19 Number of scatterers: 34405 At special positions: 0 Unit cell: (165.133, 160.877, 213.651, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 197 16.00 P 44 15.00 O 6633 8.00 N 6040 7.00 C 21491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8014 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 49 sheets defined 35.0% alpha, 18.6% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'L' and resid 92 through 110 removed outlier: 3.510A pdb=" N CYS L 96 " --> pdb=" O ASP L 92 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 108 " --> pdb=" O GLN L 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE L 110 " --> pdb=" O PHE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 149 removed outlier: 3.829A pdb=" N ALA L 136 " --> pdb=" O GLY L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 178 Processing helix chain 'L' and resid 208 through 242 removed outlier: 3.673A pdb=" N THR L 225 " --> pdb=" O ARG L 221 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU L 226 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL L 230 " --> pdb=" O LEU L 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 21 removed outlier: 3.686A pdb=" N TYR N 14 " --> pdb=" O PRO N 10 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE N 17 " --> pdb=" O TYR N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 117 removed outlier: 3.873A pdb=" N ILE N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN N 117 " --> pdb=" O ILE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 123 Processing helix chain 'N' and resid 147 through 161 removed outlier: 3.781A pdb=" N ALA N 151 " --> pdb=" O ASN N 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 218 Processing helix chain 'N' and resid 244 through 270 removed outlier: 3.540A pdb=" N SER N 253 " --> pdb=" O GLN N 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG N 254 " --> pdb=" O ASP N 250 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR N 257 " --> pdb=" O SER N 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 103 removed outlier: 3.933A pdb=" N LEU O 97 " --> pdb=" O SER O 93 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE O 98 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 111 removed outlier: 3.571A pdb=" N LEU O 110 " --> pdb=" O LEU O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 145 removed outlier: 3.755A pdb=" N CYS O 132 " --> pdb=" O SER O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 177 removed outlier: 3.546A pdb=" N GLU O 176 " --> pdb=" O LYS O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 232 removed outlier: 4.115A pdb=" N GLN O 218 " --> pdb=" O GLN O 214 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL O 220 " --> pdb=" O ALA O 216 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 222 " --> pdb=" O GLN O 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 147 through 161 removed outlier: 3.532A pdb=" N ALA F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 221 Processing helix chain 'F' and resid 248 through 280 removed outlier: 3.845A pdb=" N ILE F 252 " --> pdb=" O ASP F 248 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 253 " --> pdb=" O PRO F 249 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU F 257 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 146 No H-bonds generated for 'chain 'H' and resid 144 through 146' Processing helix chain 'H' and resid 203 through 211 removed outlier: 3.624A pdb=" N ILE H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 225 removed outlier: 3.661A pdb=" N LEU H 224 " --> pdb=" O GLU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 255 removed outlier: 4.048A pdb=" N GLU H 255 " --> pdb=" O ALA H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 275 removed outlier: 4.296A pdb=" N SER H 275 " --> pdb=" O ARG H 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.552A pdb=" N HIS A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.022A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.680A pdb=" N ASN A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 3.790A pdb=" N LEU A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 424 through 428 removed outlier: 4.014A pdb=" N TYR A 427 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.387A pdb=" N TRP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.806A pdb=" N PHE A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.714A pdb=" N LYS A 525 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 558 Processing helix chain 'A' and resid 575 through 585 removed outlier: 4.265A pdb=" N ASP A 580 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 583 " --> pdb=" O CYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 removed outlier: 3.774A pdb=" N SER A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.673A pdb=" N GLN A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 630 removed outlier: 4.013A pdb=" N LEU A 627 " --> pdb=" O HIS A 623 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 653 removed outlier: 3.627A pdb=" N ILE A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 702 removed outlier: 4.027A pdb=" N GLN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.918A pdb=" N LEU A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.602A pdb=" N ILE A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 778 through 794 removed outlier: 3.936A pdb=" N GLY A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 832 removed outlier: 3.540A pdb=" N GLU A 831 " --> pdb=" O ARG A 827 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.557A pdb=" N ARG A 888 " --> pdb=" O PRO A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 936 through 948 Processing helix chain 'A' and resid 958 through 975 Processing helix chain 'A' and resid 992 through 1010 Processing helix chain 'A' and resid 1019 through 1044 Processing helix chain 'A' and resid 1045 through 1049 Processing helix chain 'A' and resid 1051 through 1065 removed outlier: 3.544A pdb=" N VAL A1061 " --> pdb=" O GLN A1057 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A1062 " --> pdb=" O ARG A1058 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 removed outlier: 3.872A pdb=" N ALA A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 removed outlier: 3.597A pdb=" N GLU A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1112 removed outlier: 4.457A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1116 Processing helix chain 'A' and resid 1130 through 1135 Processing helix chain 'A' and resid 1135 through 1151 removed outlier: 4.338A pdb=" N VAL A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A1147 " --> pdb=" O LYS A1143 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A1148 " --> pdb=" O ARG A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1164 removed outlier: 3.715A pdb=" N GLU A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1179 Processing helix chain 'A' and resid 1181 through 1189 removed outlier: 3.556A pdb=" N LEU A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A1187 " --> pdb=" O SER A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1218 removed outlier: 4.294A pdb=" N ARG A1198 " --> pdb=" O GLY A1194 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A1205 " --> pdb=" O GLN A1201 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A1206 " --> pdb=" O ARG A1202 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A1211 " --> pdb=" O CYS A1207 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1234 removed outlier: 3.504A pdb=" N GLY A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A1227 " --> pdb=" O GLY A1223 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A1234 " --> pdb=" O ALA A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1241 removed outlier: 4.163A pdb=" N ALA A1241 " --> pdb=" O VAL A1238 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 131 removed outlier: 3.891A pdb=" N ALA G 129 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 172 removed outlier: 3.547A pdb=" N LEU G 169 " --> pdb=" O ALA G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 Processing helix chain 'G' and resid 235 through 251 removed outlier: 3.874A pdb=" N GLU G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 269 removed outlier: 3.704A pdb=" N LEU G 255 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 259 " --> pdb=" O LEU G 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 135 removed outlier: 4.109A pdb=" N LEU I 129 " --> pdb=" O ALA I 125 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA I 130 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY I 133 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE I 134 " --> pdb=" O ALA I 130 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU I 135 " --> pdb=" O MET I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 248 removed outlier: 3.614A pdb=" N ARG I 231 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL I 233 " --> pdb=" O ALA I 229 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN I 247 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG I 248 " --> pdb=" O LEU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 263 Processing helix chain 'I' and resid 273 through 293 removed outlier: 3.536A pdb=" N MET I 277 " --> pdb=" O LYS I 273 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU I 278 " --> pdb=" O PRO I 274 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 568 Processing helix chain 'E' and resid 616 through 629 Processing helix chain 'K' and resid 8 through 21 removed outlier: 3.891A pdb=" N ARG K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 113 Processing helix chain 'K' and resid 144 through 158 removed outlier: 3.724A pdb=" N ALA K 148 " --> pdb=" O ASN K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 216 Processing helix chain 'K' and resid 244 through 279 removed outlier: 3.884A pdb=" N LEU K 248 " --> pdb=" O LYS K 244 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY K 279 " --> pdb=" O VAL K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 288 Processing helix chain 'K' and resid 307 through 318 Processing helix chain 'M' and resid 63 through 68 Processing helix chain 'M' and resid 69 through 73 Processing helix chain 'M' and resid 85 through 95 Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 118 through 122 removed outlier: 3.574A pdb=" N GLN M 122 " --> pdb=" O ASN M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 154 Processing helix chain 'M' and resid 167 through 173 Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 184 through 193 Processing helix chain 'M' and resid 196 through 219 removed outlier: 3.607A pdb=" N ASN M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 240 Processing helix chain 'M' and resid 300 through 304 removed outlier: 3.937A pdb=" N TRP M 304 " --> pdb=" O LYS M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 355 Processing helix chain 'M' and resid 383 through 387 removed outlier: 3.753A pdb=" N LEU M 387 " --> pdb=" O ALA M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 431 removed outlier: 3.789A pdb=" N GLU M 423 " --> pdb=" O ASP M 419 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 445 removed outlier: 4.116A pdb=" N GLU M 445 " --> pdb=" O ALA M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 458 through 465 Processing helix chain 'M' and resid 516 through 525 removed outlier: 3.791A pdb=" N ILE M 520 " --> pdb=" O SER M 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 589 through 597 Processing helix chain 'M' and resid 615 through 647 Processing helix chain 'M' and resid 675 through 700 Processing helix chain 'M' and resid 713 through 725 removed outlier: 4.316A pdb=" N PHE M 717 " --> pdb=" O HIS M 713 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU M 719 " --> pdb=" O GLU M 715 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU M 720 " --> pdb=" O PHE M 716 " (cutoff:3.500A) Processing helix chain 'M' and resid 735 through 745 Processing helix chain 'M' and resid 752 through 764 removed outlier: 4.593A pdb=" N ARG M 756 " --> pdb=" O PRO M 752 " (cutoff:3.500A) Processing helix chain 'M' and resid 773 through 777 Processing helix chain 'M' and resid 778 through 783 removed outlier: 4.148A pdb=" N HIS M 783 " --> pdb=" O GLU M 780 " (cutoff:3.500A) Processing helix chain 'M' and resid 784 through 788 Processing helix chain 'M' and resid 802 through 818 Processing helix chain 'M' and resid 829 through 863 Processing helix chain 'M' and resid 1017 through 1025 Processing helix chain 'M' and resid 1032 through 1045 Processing sheet with id=AA1, first strand: chain 'L' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'L' and resid 49 through 55 removed outlier: 3.600A pdb=" N ASP L 121 " --> pdb=" O TYR L 52 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN L 119 " --> pdb=" O PRO L 54 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU L 70 " --> pdb=" O ILE L 120 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE L 122 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN L 72 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL L 124 " --> pdb=" O ASN L 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 49 through 55 removed outlier: 3.600A pdb=" N ASP L 121 " --> pdb=" O TYR L 52 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN L 119 " --> pdb=" O PRO L 54 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL L 126 " --> pdb=" O SER L 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 167 through 170 removed outlier: 3.850A pdb=" N GLY L 162 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU L 184 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA L 185 " --> pdb=" O GLU L 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 188 through 189 removed outlier: 3.764A pdb=" N GLN L 194 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 204 through 205 removed outlier: 4.021A pdb=" N GLU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA K 224 " --> pdb=" O CYS K 232 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE K 234 " --> pdb=" O VAL K 222 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL K 222 " --> pdb=" O ILE K 234 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER K 236 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU K 220 " --> pdb=" O SER K 236 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY K 219 " --> pdb=" O PHE K 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR K 204 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.358A pdb=" N VAL N 80 " --> pdb=" O CYS N 137 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU N 139 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN N 82 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N CYS N 141 " --> pdb=" O ASN N 82 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASP N 84 " --> pdb=" O CYS N 141 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU N 131 " --> pdb=" O ILE N 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.358A pdb=" N VAL N 80 " --> pdb=" O CYS N 137 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU N 139 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN N 82 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N CYS N 141 " --> pdb=" O ASN N 82 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASP N 84 " --> pdb=" O CYS N 141 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA K 337 " --> pdb=" O VAL N 37 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR K 336 " --> pdb=" O TRP K 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP K 332 " --> pdb=" O THR K 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 166 through 170 removed outlier: 3.681A pdb=" N GLU N 167 " --> pdb=" O ASN N 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 206 through 208 removed outlier: 3.550A pdb=" N VAL N 225 " --> pdb=" O CYS N 234 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS N 234 " --> pdb=" O VAL N 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 75 through 81 removed outlier: 5.709A pdb=" N THR O 75 " --> pdb=" O ILE O 116 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL O 118 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU O 77 " --> pdb=" O VAL O 118 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU O 120 " --> pdb=" O GLU O 77 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE O 79 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL O 122 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ARG O 81 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N SER O 124 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER O 115 " --> pdb=" O PRO O 61 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR O 117 " --> pdb=" O TYR O 59 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR O 59 " --> pdb=" O THR O 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL O 119 " --> pdb=" O GLY O 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY O 57 " --> pdb=" O VAL O 119 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER O 53 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR O 52 " --> pdb=" O GLN O 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 152 through 159 removed outlier: 3.802A pdb=" N ALA O 179 " --> pdb=" O LEU O 159 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET O 194 " --> pdb=" O ALA O 184 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP O 186 " --> pdb=" O LEU O 192 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU O 192 " --> pdb=" O ASP O 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 48 through 49 removed outlier: 3.956A pdb=" N ALA F 49 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL F 60 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP F 57 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR F 78 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL F 137 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU F 80 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL F 139 " --> pdb=" O GLU F 80 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE F 82 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F 141 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASP F 84 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N GLU F 143 " --> pdb=" O ASP F 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 209 through 212 removed outlier: 4.719A pdb=" N ALA F 224 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER F 225 " --> pdb=" O LYS F 241 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS F 241 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU F 227 " --> pdb=" O MET F 239 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET F 239 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER F 229 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU G 225 " --> pdb=" O LYS F 241 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY F 243 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N ALA G 223 " --> pdb=" O GLY F 243 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN G 221 " --> pdb=" O MET G 216 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA G 214 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU G 225 " --> pdb=" O THR G 212 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR G 212 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY G 227 " --> pdb=" O GLY G 210 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY G 210 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 209 through 212 removed outlier: 4.719A pdb=" N ALA F 224 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER F 225 " --> pdb=" O LYS F 241 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS F 241 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU F 227 " --> pdb=" O MET F 239 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET F 239 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER F 229 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU G 225 " --> pdb=" O LYS F 241 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY F 243 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N ALA G 223 " --> pdb=" O GLY F 243 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN G 221 " --> pdb=" O MET G 216 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA G 214 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU G 225 " --> pdb=" O THR G 212 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR G 212 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY G 227 " --> pdb=" O GLY G 210 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY G 210 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 19 removed outlier: 7.345A pdb=" N ARG H 18 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 27 through 28 removed outlier: 3.861A pdb=" N GLY H 84 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG H 85 " --> pdb=" O ASP H 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.599A pdb=" N VAL H 131 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE H 129 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY H 165 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU H 177 " --> pdb=" O VAL H 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.599A pdb=" N VAL H 131 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE H 129 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY H 165 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 198 through 201 removed outlier: 3.630A pdb=" N ARG H 236 " --> pdb=" O GLY H 232 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP H 238 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 13 through 16 removed outlier: 6.530A pdb=" N ILE J 33 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 21 through 22 removed outlier: 6.109A pdb=" N SER J 21 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL J 55 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER J 44 " --> pdb=" O VAL J 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 93 through 94 removed outlier: 3.664A pdb=" N MET J 93 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS J 84 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR J 72 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL J 90 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE J 70 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 128 " --> pdb=" O CYS J 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 101 through 102 removed outlier: 7.183A pdb=" N LYS J 84 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR J 72 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL J 90 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE J 70 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 128 " --> pdb=" O CYS J 73 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE J 127 " --> pdb=" O VAL J 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 171 through 173 Processing sheet with id=AC8, first strand: chain 'A' and resid 284 through 286 removed outlier: 6.808A pdb=" N ILE A 285 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N SER A 479 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 328 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER A 454 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 330 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLU A 418 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 451 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL A 420 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU A 453 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE A 422 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG A 355 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 420 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 357 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE A 422 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR A 359 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 502 through 507 removed outlier: 4.433A pdb=" N GLU A 502 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 493 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS A 489 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 488 " --> pdb=" O GLY A 713 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 676 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU A 718 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 678 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL A 570 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 569 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA A 661 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL A 571 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 913 through 920 removed outlier: 4.275A pdb=" N PHE A 871 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR A 872 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 876 " --> pdb=" O LEU A 856 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU A 856 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A 843 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL A 844 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 929 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 927 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 39 through 43 removed outlier: 6.461A pdb=" N LYS G 61 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU G 145 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN G 143 " --> pdb=" O PRO G 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.625A pdb=" N GLY I 58 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 32 through 33 removed outlier: 4.409A pdb=" N LEU I 52 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 40 through 41 removed outlier: 6.126A pdb=" N MET I 40 " --> pdb=" O ILE I 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 83 through 91 removed outlier: 3.501A pdb=" N ARG I 87 " --> pdb=" O GLU I 99 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS I 97 " --> pdb=" O THR I 89 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL I 91 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG I 95 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU I 109 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER I 155 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY I 86 " --> pdb=" O ILE I 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 170 through 173 removed outlier: 3.541A pdb=" N VAL I 195 " --> pdb=" O HIS I 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.282A pdb=" N ARG K 54 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE K 77 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 134 " --> pdb=" O PHE K 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 63 through 64 Processing sheet with id=AE1, first strand: chain 'M' and resid 4 through 12 Processing sheet with id=AE2, first strand: chain 'M' and resid 58 through 60 removed outlier: 5.860A pdb=" N TYR M 58 " --> pdb=" O VAL M 161 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL M 163 " --> pdb=" O TYR M 58 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE M 60 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE M 181 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 81 through 84 removed outlier: 7.129A pdb=" N ILE M 81 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE M 117 " --> pdb=" O ILE M 81 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE M 83 " --> pdb=" O PHE M 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'M' and resid 244 through 246 removed outlier: 3.754A pdb=" N GLY M 246 " --> pdb=" O VAL M 294 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL M 294 " --> pdb=" O GLY M 246 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL M 293 " --> pdb=" O ILE M 337 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE M 337 " --> pdb=" O VAL M 293 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL M 295 " --> pdb=" O VAL M 335 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL M 335 " --> pdb=" O VAL M 295 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 248 through 250 removed outlier: 3.634A pdb=" N ILE M 277 " --> pdb=" O VAL M 261 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 346 through 348 removed outlier: 3.611A pdb=" N ILE M 377 " --> pdb=" O VAL M 367 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER M 380 " --> pdb=" O GLY M 408 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE M 410 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN M 407 " --> pdb=" O ASP M 397 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS M 409 " --> pdb=" O ARG M 395 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL M 393 " --> pdb=" O VAL M 411 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL M 413 " --> pdb=" O ARG M 391 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG M 391 " --> pdb=" O VAL M 413 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 392 " --> pdb=" O VAL M 347 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 489 through 493 removed outlier: 3.645A pdb=" N ARG M 492 " --> pdb=" O GLU M 500 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG M 556 " --> pdb=" O ILE M 582 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR M 580 " --> pdb=" O ALA M 558 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 656 through 660 removed outlier: 3.993A pdb=" N GLN M 659 " --> pdb=" O ASP M 668 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP M 668 " --> pdb=" O GLN M 659 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 706 through 708 removed outlier: 3.618A pdb=" N GLN M 708 " --> pdb=" O LEU M 770 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 770 " --> pdb=" O GLN M 708 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 879 through 882 removed outlier: 6.179A pdb=" N ILE M 880 " --> pdb=" O PHE M 891 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE M 891 " --> pdb=" O ILE M 880 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER M 882 " --> pdb=" O LEU M 889 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY M 899 " --> pdb=" O LEU M 890 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 911 through 913 Processing sheet with id=AF3, first strand: chain 'M' and resid 924 through 928 Processing sheet with id=AF4, first strand: chain 'M' and resid 953 through 958 removed outlier: 3.506A pdb=" N THR M 966 " --> pdb=" O GLN M 958 " (cutoff:3.500A) 1282 hydrogen bonds defined for protein. 3648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 7.83 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10892 1.34 - 1.46: 5365 1.46 - 1.58: 18435 1.58 - 1.70: 87 1.70 - 1.82: 289 Bond restraints: 35068 Sorted by residual: bond pdb=" CG MET A1037 " pdb=" SD MET A1037 " ideal model delta sigma weight residual 1.803 1.759 0.044 2.50e-02 1.60e+03 3.14e+00 bond pdb=" CG GLU M 201 " pdb=" CD GLU M 201 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" C THR E 608 " pdb=" N PRO E 609 " ideal model delta sigma weight residual 1.334 1.367 -0.034 2.34e-02 1.83e+03 2.06e+00 bond pdb=" CA GLN O 49 " pdb=" CB GLN O 49 " ideal model delta sigma weight residual 1.531 1.576 -0.045 3.28e-02 9.30e+02 1.91e+00 bond pdb=" CG LEU I 244 " pdb=" CD1 LEU I 244 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 ... (remaining 35063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 47317 3.97 - 7.94: 248 7.94 - 11.91: 23 11.91 - 15.88: 4 15.88 - 19.85: 1 Bond angle restraints: 47593 Sorted by residual: angle pdb=" C VAL I 63 " pdb=" N ASN I 64 " pdb=" CA ASN I 64 " ideal model delta sigma weight residual 121.54 141.39 -19.85 1.91e+00 2.74e-01 1.08e+02 angle pdb=" C PRO M 61 " pdb=" N ASP M 62 " pdb=" CA ASP M 62 " ideal model delta sigma weight residual 120.89 110.13 10.76 1.50e+00 4.44e-01 5.14e+01 angle pdb=" C ASP K 304 " pdb=" N THR K 305 " pdb=" CA THR K 305 " ideal model delta sigma weight residual 122.27 111.71 10.56 1.85e+00 2.92e-01 3.26e+01 angle pdb=" C PRO K 302 " pdb=" N ILE K 303 " pdb=" CA ILE K 303 " ideal model delta sigma weight residual 121.97 111.96 10.01 1.80e+00 3.09e-01 3.09e+01 angle pdb=" C MET M 766 " pdb=" N SER M 767 " pdb=" CA SER M 767 " ideal model delta sigma weight residual 122.12 131.88 -9.76 1.76e+00 3.23e-01 3.08e+01 ... (remaining 47588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 21058 35.05 - 70.09: 499 70.09 - 105.14: 39 105.14 - 140.18: 2 140.18 - 175.23: 5 Dihedral angle restraints: 21603 sinusoidal: 9198 harmonic: 12405 Sorted by residual: dihedral pdb=" CA ALA G 91 " pdb=" C ALA G 91 " pdb=" N LEU G 92 " pdb=" CA LEU G 92 " ideal model delta harmonic sigma weight residual -180.00 -88.52 -91.48 0 5.00e+00 4.00e-02 3.35e+02 dihedral pdb=" CA ILE K 303 " pdb=" C ILE K 303 " pdb=" N ASP K 304 " pdb=" CA ASP K 304 " ideal model delta harmonic sigma weight residual 180.00 124.81 55.19 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA ALA M 545 " pdb=" C ALA M 545 " pdb=" N ASP M 546 " pdb=" CA ASP M 546 " ideal model delta harmonic sigma weight residual 180.00 132.03 47.97 0 5.00e+00 4.00e-02 9.21e+01 ... (remaining 21600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4076 0.046 - 0.092: 1049 0.092 - 0.138: 322 0.138 - 0.185: 29 0.185 - 0.231: 9 Chirality restraints: 5485 Sorted by residual: chirality pdb=" CA PRO A1018 " pdb=" N PRO A1018 " pdb=" C PRO A1018 " pdb=" CB PRO A1018 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA THR E 608 " pdb=" N THR E 608 " pdb=" C THR E 608 " pdb=" CB THR E 608 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA MET A1037 " pdb=" N MET A1037 " pdb=" C MET A1037 " pdb=" CB MET A1037 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 5482 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 91 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO K 92 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO K 92 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO K 92 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 601 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C HIS A 601 " -0.070 2.00e-02 2.50e+03 pdb=" O HIS A 601 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 602 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 9 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO J 10 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO J 10 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO J 10 " -0.043 5.00e-02 4.00e+02 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 508 2.65 - 3.21: 31192 3.21 - 3.78: 49074 3.78 - 4.34: 67023 4.34 - 4.90: 109954 Nonbonded interactions: 257751 Sorted by model distance: nonbonded pdb=" OG1 THR M 488 " pdb=" O HIS M 504 " model vdw 2.088 3.040 nonbonded pdb=" NE2 GLN O 49 " pdb=" OD1 ASP O 168 " model vdw 2.141 3.120 nonbonded pdb=" OD1 ASN M 251 " pdb=" N LYS M 252 " model vdw 2.183 3.120 nonbonded pdb=" NH1 ARG O 230 " pdb=" O ALA K 295 " model vdw 2.183 3.120 nonbonded pdb=" OH TYR A 748 " pdb=" OE1 GLN A1149 " model vdw 2.197 3.040 ... (remaining 257746 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 52.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 30.080 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.003 0.056 35068 Z= 0.135 Angle : 0.800 19.845 47593 Z= 0.433 Chirality : 0.046 0.231 5485 Planarity : 0.006 0.108 6036 Dihedral : 15.592 175.226 13589 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.12), residues: 4260 helix: -1.29 (0.13), residues: 1313 sheet: -1.23 (0.19), residues: 745 loop : -2.83 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 285 TYR 0.022 0.001 TYR M 577 PHE 0.028 0.001 PHE A 377 TRP 0.029 0.001 TRP A1176 HIS 0.007 0.001 HIS M 253 Details of bonding type rmsd covalent geometry : bond 0.00274 (35068) covalent geometry : angle 0.79995 (47593) hydrogen bonds : bond 0.19684 ( 1248) hydrogen bonds : angle 7.54061 ( 3648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 94 LYS cc_start: 0.8869 (mmpt) cc_final: 0.8583 (mmmt) REVERT: A 529 MET cc_start: 0.8298 (pmm) cc_final: 0.8089 (pmm) REVERT: A 667 MET cc_start: 0.6727 (ppp) cc_final: 0.6527 (tmm) REVERT: I 219 PHE cc_start: 0.7205 (m-80) cc_final: 0.6939 (m-80) REVERT: M 158 MET cc_start: 0.8019 (tpt) cc_final: 0.7289 (tmm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1770 time to fit residues: 60.6761 Evaluate side-chains 155 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 HIS F 162 ASN H 171 ASN H 252 ASN J 62 GLN K 168 GLN M 215 ASN M 472 HIS M 619 GLN M 667 HIS ** M 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1016 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.068341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048636 restraints weight = 188993.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049858 restraints weight = 105303.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.050658 restraints weight = 72928.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051156 restraints weight = 57697.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051504 restraints weight = 49841.407| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 35068 Z= 0.240 Angle : 0.713 11.542 47593 Z= 0.369 Chirality : 0.045 0.189 5485 Planarity : 0.005 0.073 6036 Dihedral : 12.069 179.754 5379 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.11 % Favored : 90.85 % Rotamer: Outliers : 0.79 % Allowed : 7.61 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.12), residues: 4260 helix: -0.19 (0.14), residues: 1372 sheet: -1.33 (0.18), residues: 781 loop : -2.60 (0.12), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 734 TYR 0.025 0.002 TYR F 187 PHE 0.018 0.002 PHE A 377 TRP 0.015 0.002 TRP M 63 HIS 0.009 0.001 HIS M 667 Details of bonding type rmsd covalent geometry : bond 0.00551 (35068) covalent geometry : angle 0.71286 (47593) hydrogen bonds : bond 0.05305 ( 1248) hydrogen bonds : angle 5.39348 ( 3648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 94 LYS cc_start: 0.8984 (mmpt) cc_final: 0.8777 (mmmt) REVERT: A 667 MET cc_start: 0.7211 (ppp) cc_final: 0.6948 (tmm) REVERT: A 1180 MET cc_start: 0.8690 (ttt) cc_final: 0.8212 (tmm) REVERT: I 219 PHE cc_start: 0.7462 (m-80) cc_final: 0.7157 (m-80) REVERT: M 86 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8431 (m) REVERT: M 158 MET cc_start: 0.8246 (tpt) cc_final: 0.7998 (mmm) outliers start: 29 outliers final: 18 residues processed: 171 average time/residue: 0.1719 time to fit residues: 50.2757 Evaluate side-chains 164 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 517 TYR Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 916 ASP Chi-restraints excluded: chain M residue 1016 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 348 optimal weight: 3.9990 chunk 272 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 264 optimal weight: 0.6980 chunk 406 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 293 optimal weight: 0.0470 chunk 39 optimal weight: 0.7980 chunk 357 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN A 302 GLN M 784 HIS ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 963 HIS M1016 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.069317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049595 restraints weight = 185567.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.050849 restraints weight = 103030.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051659 restraints weight = 70785.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052192 restraints weight = 55803.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.052537 restraints weight = 48015.300| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35068 Z= 0.117 Angle : 0.593 10.581 47593 Z= 0.305 Chirality : 0.042 0.167 5485 Planarity : 0.004 0.073 6036 Dihedral : 11.870 177.917 5379 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 1.09 % Allowed : 10.42 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.13), residues: 4260 helix: 0.40 (0.14), residues: 1386 sheet: -0.97 (0.19), residues: 773 loop : -2.35 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 131 TYR 0.016 0.001 TYR I 76 PHE 0.012 0.001 PHE A 377 TRP 0.012 0.001 TRP I 96 HIS 0.007 0.001 HIS M 200 Details of bonding type rmsd covalent geometry : bond 0.00260 (35068) covalent geometry : angle 0.59336 (47593) hydrogen bonds : bond 0.04304 ( 1248) hydrogen bonds : angle 4.82745 ( 3648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 172 MET cc_start: 0.7591 (mtp) cc_final: 0.7385 (mtp) REVERT: A 667 MET cc_start: 0.7167 (ppp) cc_final: 0.6892 (tmm) REVERT: A 1180 MET cc_start: 0.8821 (ttt) cc_final: 0.8140 (tmm) REVERT: G 251 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8558 (mp) REVERT: I 219 PHE cc_start: 0.7472 (m-80) cc_final: 0.7110 (m-80) REVERT: M 158 MET cc_start: 0.8248 (tpt) cc_final: 0.7983 (mmm) REVERT: M 201 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8823 (pm20) outliers start: 40 outliers final: 16 residues processed: 188 average time/residue: 0.1793 time to fit residues: 57.4347 Evaluate side-chains 167 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain E residue 620 ILE Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 201 GLU Chi-restraints excluded: chain M residue 517 TYR Chi-restraints excluded: chain M residue 916 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 392 optimal weight: 0.4980 chunk 264 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 chunk 146 optimal weight: 0.3980 chunk 425 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 ASN M 431 ASN M 472 HIS M 708 GLN ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.068995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049238 restraints weight = 185253.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050474 restraints weight = 103152.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.051285 restraints weight = 71364.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051816 restraints weight = 56411.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052165 restraints weight = 48561.179| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35068 Z= 0.124 Angle : 0.569 9.938 47593 Z= 0.293 Chirality : 0.042 0.174 5485 Planarity : 0.004 0.061 6036 Dihedral : 11.694 177.583 5379 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer: Outliers : 1.31 % Allowed : 12.08 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.13), residues: 4260 helix: 0.75 (0.14), residues: 1383 sheet: -0.87 (0.18), residues: 791 loop : -2.17 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 15 TYR 0.018 0.001 TYR G 20 PHE 0.022 0.001 PHE M 730 TRP 0.012 0.001 TRP I 96 HIS 0.007 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00281 (35068) covalent geometry : angle 0.56907 (47593) hydrogen bonds : bond 0.03977 ( 1248) hydrogen bonds : angle 4.52179 ( 3648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: L 94 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8648 (mmmt) REVERT: N 180 ASN cc_start: 0.9120 (m110) cc_final: 0.8865 (p0) REVERT: A 667 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.7022 (ppp) REVERT: A 830 MET cc_start: 0.6394 (mmm) cc_final: 0.6163 (mmm) REVERT: A 1180 MET cc_start: 0.8835 (ttt) cc_final: 0.8160 (tmm) REVERT: G 251 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8550 (mp) REVERT: I 1 MET cc_start: 0.5630 (tpp) cc_final: 0.4810 (mmm) REVERT: I 219 PHE cc_start: 0.7518 (m-80) cc_final: 0.7121 (m-80) REVERT: E 614 SER cc_start: 0.7236 (m) cc_final: 0.6691 (p) REVERT: K 104 ARG cc_start: 0.7933 (mmt-90) cc_final: 0.7611 (mmm-85) REVERT: M 158 MET cc_start: 0.8234 (tpt) cc_final: 0.7971 (mmm) REVERT: M 282 MET cc_start: 0.8103 (mpp) cc_final: 0.7806 (tpp) REVERT: M 745 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7166 (p0) outliers start: 48 outliers final: 22 residues processed: 195 average time/residue: 0.1636 time to fit residues: 54.7633 Evaluate side-chains 172 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain E residue 620 ILE Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 517 TYR Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 745 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 201 optimal weight: 1.9990 chunk 419 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 380 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 190 optimal weight: 0.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A1201 GLN M 361 ASN M 382 GLN M 472 HIS ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.068180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048412 restraints weight = 186850.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049630 restraints weight = 104339.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050427 restraints weight = 72515.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050956 restraints weight = 57444.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051283 restraints weight = 49574.762| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35068 Z= 0.154 Angle : 0.584 10.911 47593 Z= 0.300 Chirality : 0.042 0.179 5485 Planarity : 0.004 0.062 6036 Dihedral : 11.678 179.341 5379 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 1.45 % Allowed : 13.83 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.13), residues: 4260 helix: 0.87 (0.14), residues: 1386 sheet: -0.73 (0.19), residues: 776 loop : -2.12 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M1026 TYR 0.018 0.001 TYR I 76 PHE 0.016 0.001 PHE M 730 TRP 0.012 0.001 TRP I 96 HIS 0.007 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00353 (35068) covalent geometry : angle 0.58430 (47593) hydrogen bonds : bond 0.04149 ( 1248) hydrogen bonds : angle 4.48790 ( 3648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5991 (tt) REVERT: L 94 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8718 (mmmt) REVERT: H 178 MET cc_start: 0.8482 (ptm) cc_final: 0.8256 (ptm) REVERT: A 667 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6767 (tmm) REVERT: A 1180 MET cc_start: 0.8867 (ttt) cc_final: 0.8160 (tmm) REVERT: G 251 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8527 (mp) REVERT: I 1 MET cc_start: 0.5733 (tpp) cc_final: 0.5260 (mmm) REVERT: E 614 SER cc_start: 0.7081 (m) cc_final: 0.6485 (p) REVERT: M 158 MET cc_start: 0.8299 (tpt) cc_final: 0.8016 (mmm) REVERT: M 201 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8705 (pm20) REVERT: M 282 MET cc_start: 0.8122 (mpp) cc_final: 0.7804 (tpp) REVERT: M 745 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7235 (p0) outliers start: 53 outliers final: 30 residues processed: 191 average time/residue: 0.1638 time to fit residues: 54.0758 Evaluate side-chains 177 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain E residue 620 ILE Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 201 GLU Chi-restraints excluded: chain M residue 489 LEU Chi-restraints excluded: chain M residue 504 HIS Chi-restraints excluded: chain M residue 517 TYR Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 745 ASN Chi-restraints excluded: chain M residue 916 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 224 optimal weight: 0.0370 chunk 66 optimal weight: 0.9990 chunk 334 optimal weight: 0.0070 chunk 280 optimal weight: 3.9990 chunk 137 optimal weight: 0.0050 chunk 150 optimal weight: 4.9990 chunk 345 optimal weight: 0.9980 chunk 136 optimal weight: 0.0570 chunk 387 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 180 ASN ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN A 495 ASN A1201 GLN M 34 HIS ** M 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.069346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049564 restraints weight = 182331.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050817 restraints weight = 101070.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051638 restraints weight = 69778.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052178 restraints weight = 55067.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052514 restraints weight = 47367.892| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35068 Z= 0.098 Angle : 0.546 9.468 47593 Z= 0.278 Chirality : 0.041 0.184 5485 Planarity : 0.004 0.058 6036 Dihedral : 11.577 177.992 5379 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 1.12 % Allowed : 14.76 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.13), residues: 4260 helix: 1.17 (0.14), residues: 1381 sheet: -0.70 (0.19), residues: 782 loop : -1.99 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M1026 TYR 0.019 0.001 TYR G 20 PHE 0.011 0.001 PHE A 377 TRP 0.011 0.001 TRP I 96 HIS 0.005 0.001 HIS M 638 Details of bonding type rmsd covalent geometry : bond 0.00211 (35068) covalent geometry : angle 0.54557 (47593) hydrogen bonds : bond 0.03525 ( 1248) hydrogen bonds : angle 4.21683 ( 3648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 94 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8638 (mmmt) REVERT: J 106 GLU cc_start: 0.8047 (mp0) cc_final: 0.7659 (mp0) REVERT: A 830 MET cc_start: 0.6014 (mmm) cc_final: 0.5689 (mmm) REVERT: A 1180 MET cc_start: 0.8816 (ttt) cc_final: 0.8109 (tmm) REVERT: I 1 MET cc_start: 0.5723 (tpp) cc_final: 0.5200 (mmm) REVERT: I 114 ASN cc_start: 0.8256 (m-40) cc_final: 0.7377 (t0) REVERT: E 614 SER cc_start: 0.6983 (m) cc_final: 0.6391 (p) REVERT: K 104 ARG cc_start: 0.7879 (mmt-90) cc_final: 0.7526 (mmm-85) REVERT: M 158 MET cc_start: 0.8256 (tpt) cc_final: 0.7953 (mmm) REVERT: M 282 MET cc_start: 0.8103 (mpp) cc_final: 0.7786 (tpp) REVERT: M 638 HIS cc_start: 0.7768 (m90) cc_final: 0.7278 (t70) REVERT: M 745 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7301 (p0) outliers start: 41 outliers final: 26 residues processed: 194 average time/residue: 0.1609 time to fit residues: 53.5913 Evaluate side-chains 182 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain M residue 472 HIS Chi-restraints excluded: chain M residue 489 LEU Chi-restraints excluded: chain M residue 504 HIS Chi-restraints excluded: chain M residue 517 TYR Chi-restraints excluded: chain M residue 745 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 308 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 423 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 418 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 288 optimal weight: 0.6980 chunk 357 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 619 GLN ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.068532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.048718 restraints weight = 188408.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049968 restraints weight = 104773.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050744 restraints weight = 72527.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051292 restraints weight = 57742.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051635 restraints weight = 49778.216| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35068 Z= 0.129 Angle : 0.558 9.864 47593 Z= 0.285 Chirality : 0.041 0.191 5485 Planarity : 0.004 0.055 6036 Dihedral : 11.565 178.868 5379 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.42 % Rotamer: Outliers : 1.39 % Allowed : 15.00 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.13), residues: 4260 helix: 1.22 (0.14), residues: 1387 sheet: -0.62 (0.19), residues: 783 loop : -1.99 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M1026 TYR 0.014 0.001 TYR I 76 PHE 0.019 0.001 PHE M 730 TRP 0.011 0.001 TRP I 96 HIS 0.006 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00295 (35068) covalent geometry : angle 0.55844 (47593) hydrogen bonds : bond 0.03729 ( 1248) hydrogen bonds : angle 4.20516 ( 3648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5960 (tt) REVERT: L 94 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8798 (mmmt) REVERT: A 624 MET cc_start: 0.7605 (ttp) cc_final: 0.7090 (ptm) REVERT: A 667 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7145 (tmm) REVERT: A 1180 MET cc_start: 0.8821 (ttt) cc_final: 0.8190 (tmm) REVERT: I 1 MET cc_start: 0.5878 (tpp) cc_final: 0.5079 (mmm) REVERT: I 114 ASN cc_start: 0.8281 (m-40) cc_final: 0.7443 (t0) REVERT: M 158 MET cc_start: 0.8264 (tpt) cc_final: 0.7967 (mmm) REVERT: M 282 MET cc_start: 0.8069 (mpp) cc_final: 0.7761 (tpp) REVERT: M 638 HIS cc_start: 0.7794 (m90) cc_final: 0.7311 (t70) REVERT: M 745 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7340 (p0) outliers start: 51 outliers final: 34 residues processed: 193 average time/residue: 0.1661 time to fit residues: 55.7294 Evaluate side-chains 182 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain M residue 472 HIS Chi-restraints excluded: chain M residue 489 LEU Chi-restraints excluded: chain M residue 504 HIS Chi-restraints excluded: chain M residue 517 TYR Chi-restraints excluded: chain M residue 745 ASN Chi-restraints excluded: chain M residue 929 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 358 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 356 optimal weight: 0.9990 chunk 62 optimal weight: 0.0000 chunk 313 optimal weight: 3.9990 chunk 414 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 305 optimal weight: 0.0060 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 GLN ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.068631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048917 restraints weight = 186186.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050161 restraints weight = 103197.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050943 restraints weight = 71253.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051504 restraints weight = 56530.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.051849 restraints weight = 48472.054| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35068 Z= 0.113 Angle : 0.557 13.488 47593 Z= 0.281 Chirality : 0.041 0.299 5485 Planarity : 0.004 0.055 6036 Dihedral : 11.536 178.080 5379 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.97 % Favored : 92.98 % Rotamer: Outliers : 1.39 % Allowed : 15.30 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 4260 helix: 1.33 (0.14), residues: 1380 sheet: -0.64 (0.19), residues: 803 loop : -1.91 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M1026 TYR 0.018 0.001 TYR I 76 PHE 0.012 0.001 PHE A 377 TRP 0.011 0.001 TRP I 96 HIS 0.006 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00257 (35068) covalent geometry : angle 0.55693 (47593) hydrogen bonds : bond 0.03619 ( 1248) hydrogen bonds : angle 4.14506 ( 3648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5977 (tt) REVERT: H 178 MET cc_start: 0.8471 (ptm) cc_final: 0.8220 (ptm) REVERT: A 624 MET cc_start: 0.7603 (ttp) cc_final: 0.7102 (ptm) REVERT: A 1069 ASP cc_start: 0.8091 (p0) cc_final: 0.7887 (p0) REVERT: A 1180 MET cc_start: 0.8810 (ttt) cc_final: 0.8180 (tmm) REVERT: I 1 MET cc_start: 0.5888 (tpp) cc_final: 0.5094 (mmm) REVERT: I 114 ASN cc_start: 0.8229 (m-40) cc_final: 0.7429 (t0) REVERT: I 252 TYR cc_start: 0.8173 (p90) cc_final: 0.7964 (p90) REVERT: M 158 MET cc_start: 0.8282 (tpt) cc_final: 0.7957 (mmm) REVERT: M 282 MET cc_start: 0.8043 (mpp) cc_final: 0.7742 (tpp) REVERT: M 638 HIS cc_start: 0.7820 (m90) cc_final: 0.7383 (t70) REVERT: M 745 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7342 (p0) outliers start: 51 outliers final: 39 residues processed: 195 average time/residue: 0.1682 time to fit residues: 56.5251 Evaluate side-chains 186 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain M residue 201 GLU Chi-restraints excluded: chain M residue 472 HIS Chi-restraints excluded: chain M residue 504 HIS Chi-restraints excluded: chain M residue 517 TYR Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 745 ASN Chi-restraints excluded: chain M residue 916 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 143 optimal weight: 0.0020 chunk 91 optimal weight: 0.5980 chunk 300 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 294 optimal weight: 0.0470 chunk 123 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 329 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 GLN ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.069179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049480 restraints weight = 184097.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050733 restraints weight = 101954.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051566 restraints weight = 70411.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052101 restraints weight = 55458.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.052441 restraints weight = 47743.065| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35068 Z= 0.099 Angle : 0.561 12.244 47593 Z= 0.281 Chirality : 0.041 0.239 5485 Planarity : 0.004 0.054 6036 Dihedral : 11.483 177.903 5379 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.50 % Favored : 93.45 % Rotamer: Outliers : 1.15 % Allowed : 15.74 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.13), residues: 4260 helix: 1.50 (0.14), residues: 1373 sheet: -0.55 (0.19), residues: 799 loop : -1.85 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 415 TYR 0.013 0.001 TYR I 76 PHE 0.013 0.001 PHE M 730 TRP 0.012 0.001 TRP M 563 HIS 0.006 0.001 HIS M 638 Details of bonding type rmsd covalent geometry : bond 0.00222 (35068) covalent geometry : angle 0.56057 (47593) hydrogen bonds : bond 0.03359 ( 1248) hydrogen bonds : angle 4.02649 ( 3648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 1.164 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: L 48 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5935 (tt) REVERT: L 97 GLU cc_start: 0.7764 (pt0) cc_final: 0.7540 (pt0) REVERT: H 178 MET cc_start: 0.8461 (ptm) cc_final: 0.8241 (ptm) REVERT: A 624 MET cc_start: 0.7521 (ttp) cc_final: 0.7031 (ptm) REVERT: A 1180 MET cc_start: 0.8786 (ttt) cc_final: 0.8153 (tmm) REVERT: I 1 MET cc_start: 0.5961 (tpp) cc_final: 0.5199 (mmm) REVERT: I 114 ASN cc_start: 0.8225 (m-40) cc_final: 0.7458 (t0) REVERT: M 158 MET cc_start: 0.8293 (tpt) cc_final: 0.7999 (mmm) REVERT: M 282 MET cc_start: 0.8024 (mpp) cc_final: 0.7717 (tpp) REVERT: M 638 HIS cc_start: 0.7809 (m90) cc_final: 0.7452 (t70) outliers start: 42 outliers final: 33 residues processed: 200 average time/residue: 0.1663 time to fit residues: 57.2830 Evaluate side-chains 188 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 266 HIS Chi-restraints excluded: chain E residue 620 ILE Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain M residue 201 GLU Chi-restraints excluded: chain M residue 472 HIS Chi-restraints excluded: chain M residue 504 HIS Chi-restraints excluded: chain M residue 745 ASN Chi-restraints excluded: chain M residue 929 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 396 optimal weight: 0.0060 chunk 21 optimal weight: 0.5980 chunk 168 optimal weight: 0.0770 chunk 342 optimal weight: 4.9990 chunk 67 optimal weight: 0.0570 chunk 150 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 392 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 overall best weight: 0.2672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.069473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049764 restraints weight = 186625.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051030 restraints weight = 102697.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.051865 restraints weight = 70678.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052419 restraints weight = 55626.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.052762 restraints weight = 47748.094| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35068 Z= 0.097 Angle : 0.564 12.397 47593 Z= 0.282 Chirality : 0.041 0.260 5485 Planarity : 0.004 0.053 6036 Dihedral : 11.428 177.392 5379 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 1.04 % Allowed : 16.07 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.13), residues: 4260 helix: 1.64 (0.14), residues: 1372 sheet: -0.47 (0.19), residues: 802 loop : -1.80 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M1026 TYR 0.012 0.001 TYR I 76 PHE 0.011 0.001 PHE A 377 TRP 0.013 0.001 TRP M 563 HIS 0.006 0.001 HIS M 667 Details of bonding type rmsd covalent geometry : bond 0.00217 (35068) covalent geometry : angle 0.56428 (47593) hydrogen bonds : bond 0.03216 ( 1248) hydrogen bonds : angle 3.94064 ( 3648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5914 (tt) REVERT: A 624 MET cc_start: 0.7490 (ttp) cc_final: 0.7053 (ptm) REVERT: A 1180 MET cc_start: 0.8786 (ttt) cc_final: 0.8160 (tmm) REVERT: I 1 MET cc_start: 0.5842 (tpp) cc_final: 0.5074 (mmm) REVERT: I 114 ASN cc_start: 0.8222 (m-40) cc_final: 0.7457 (t0) REVERT: I 252 TYR cc_start: 0.8015 (p90) cc_final: 0.7563 (p90) REVERT: M 158 MET cc_start: 0.8296 (tpt) cc_final: 0.7955 (mmm) REVERT: M 282 MET cc_start: 0.8008 (mpp) cc_final: 0.7683 (tpp) REVERT: M 638 HIS cc_start: 0.7836 (m90) cc_final: 0.7495 (t70) outliers start: 38 outliers final: 33 residues processed: 199 average time/residue: 0.1705 time to fit residues: 58.6984 Evaluate side-chains 192 residues out of total 3667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 266 HIS Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain M residue 472 HIS Chi-restraints excluded: chain M residue 504 HIS Chi-restraints excluded: chain M residue 745 ASN Chi-restraints excluded: chain M residue 929 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 147 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 189 optimal weight: 0.5980 chunk 251 optimal weight: 0.5980 chunk 243 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 358 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 331 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.068479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048884 restraints weight = 185941.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.050108 restraints weight = 102887.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050914 restraints weight = 71041.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051447 restraints weight = 56157.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051748 restraints weight = 48274.709| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35068 Z= 0.127 Angle : 0.576 12.046 47593 Z= 0.290 Chirality : 0.041 0.243 5485 Planarity : 0.004 0.052 6036 Dihedral : 11.443 177.801 5379 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 1.20 % Allowed : 16.07 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.13), residues: 4260 helix: 1.60 (0.14), residues: 1374 sheet: -0.46 (0.19), residues: 806 loop : -1.79 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M1026 TYR 0.016 0.001 TYR I 76 PHE 0.014 0.001 PHE M 730 TRP 0.012 0.001 TRP M 563 HIS 0.007 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00291 (35068) covalent geometry : angle 0.57619 (47593) hydrogen bonds : bond 0.03577 ( 1248) hydrogen bonds : angle 4.04440 ( 3648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6427.37 seconds wall clock time: 111 minutes 44.40 seconds (6704.40 seconds total)