Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 08:27:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4o_32310/08_2023/7w4o_32310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4o_32310/08_2023/7w4o_32310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4o_32310/08_2023/7w4o_32310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4o_32310/08_2023/7w4o_32310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4o_32310/08_2023/7w4o_32310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4o_32310/08_2023/7w4o_32310_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.175 sd= 0.332 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 20 5.49 5 Mg 8 5.21 5 S 312 5.16 5 Cl 4 4.86 5 C 35460 2.51 5 N 9292 2.21 5 O 9652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 54748 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2533 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 11077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1411, 11077 Classifications: {'peptide': 1411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 45, 'TRANS': 1365} Chain breaks: 7 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2533 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 11077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1411, 11077 Classifications: {'peptide': 1411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 45, 'TRANS': 1365} Chain breaks: 7 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2533 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 11077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1411, 11077 Classifications: {'peptide': 1411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 45, 'TRANS': 1365} Chain breaks: 7 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "G" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2533 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 11077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1411, 11077 Classifications: {'peptide': 1411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 45, 'TRANS': 1365} Chain breaks: 7 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 19.43, per 1000 atoms: 0.35 Number of scatterers: 54748 At special positions: 0 Unit cell: (223.756, 223.756, 146.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 312 16.00 P 20 15.00 Mg 8 11.99 O 9652 8.00 N 9292 7.00 C 35460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.18 Conformation dependent library (CDL) restraints added in 6.0 seconds 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 252 helices and 44 sheets defined 57.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.38 Creating SS restraints... Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 96 removed outlier: 3.812A pdb=" N PHE A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 177 through 180 No H-bonds generated for 'chain 'A' and resid 177 through 180' Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.488A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 25 through 51 Proline residue: B 35 - end of helix Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 71 through 96 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 108 through 130 Processing helix chain 'B' and resid 133 through 159 removed outlier: 3.761A pdb=" N ILE B 137 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 138 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 192 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.953A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 240 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 328 removed outlier: 5.809A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 356 through 400 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.938A pdb=" N VAL B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 455 Proline residue: B 436 - end of helix Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 458 through 504 removed outlier: 3.903A pdb=" N LEU B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.579A pdb=" N GLU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 515 through 561 Proline residue: B 551 - end of helix Processing helix chain 'B' and resid 573 through 614 Proline residue: B 589 - end of helix removed outlier: 4.509A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 796 through 806 removed outlier: 3.559A pdb=" N MET B 801 " --> pdb=" O GLN B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 812 No H-bonds generated for 'chain 'B' and resid 809 through 812' Processing helix chain 'B' and resid 832 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 891 through 896 Proline residue: B 895 - end of helix Processing helix chain 'B' and resid 914 through 917 No H-bonds generated for 'chain 'B' and resid 914 through 917' Processing helix chain 'B' and resid 922 through 931 Processing helix chain 'B' and resid 1003 through 1008 Processing helix chain 'B' and resid 1010 through 1038 Processing helix chain 'B' and resid 1061 through 1106 removed outlier: 3.750A pdb=" N GLU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1126 removed outlier: 4.023A pdb=" N ARG B1124 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1160 removed outlier: 4.564A pdb=" N ILE B1136 " --> pdb=" O ILE B1132 " (cutoff:3.500A) Proline residue: B1137 - end of helix removed outlier: 3.552A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B1151 " --> pdb=" O THR B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1209 removed outlier: 3.773A pdb=" N LEU B1169 " --> pdb=" O VAL B1166 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 4.045A pdb=" N CYS B1175 " --> pdb=" O ALA B1172 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE B1182 " --> pdb=" O GLN B1179 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG B1183 " --> pdb=" O LYS B1180 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B1184 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER B1186 " --> pdb=" O ARG B1183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B1187 " --> pdb=" O VAL B1184 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B1190 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B1192 " --> pdb=" O LEU B1189 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B1195 " --> pdb=" O LEU B1192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B1196 " --> pdb=" O ASP B1193 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU B1198 " --> pdb=" O THR B1195 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 4.204A pdb=" N SER B1202 " --> pdb=" O PRO B1199 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B1206 " --> pdb=" O HIS B1203 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B1208 " --> pdb=" O ALA B1205 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU B1209 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1216 Processing helix chain 'B' and resid 1220 through 1273 Processing helix chain 'B' and resid 1280 through 1319 removed outlier: 3.582A pdb=" N MET B1290 " --> pdb=" O THR B1286 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN B1296 " --> pdb=" O SER B1292 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP B1297 " --> pdb=" O ASN B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1393 removed outlier: 3.652A pdb=" N SER B1389 " --> pdb=" O LYS B1385 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE B1392 " --> pdb=" O PHE B1388 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE B1393 " --> pdb=" O SER B1389 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1412 No H-bonds generated for 'chain 'B' and resid 1410 through 1412' Processing helix chain 'B' and resid 1415 through 1420 Processing helix chain 'B' and resid 1436 through 1440 Processing helix chain 'B' and resid 1448 through 1457 Processing helix chain 'B' and resid 1461 through 1466 Processing helix chain 'B' and resid 1470 through 1472 No H-bonds generated for 'chain 'B' and resid 1470 through 1472' Processing helix chain 'B' and resid 1484 through 1496 Processing helix chain 'B' and resid 1508 through 1510 No H-bonds generated for 'chain 'B' and resid 1508 through 1510' Processing helix chain 'B' and resid 1514 through 1527 removed outlier: 3.652A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1543 Processing helix chain 'B' and resid 1563 through 1566 No H-bonds generated for 'chain 'B' and resid 1563 through 1566' Processing helix chain 'B' and resid 1573 through 1579 Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 68 through 96 removed outlier: 3.812A pdb=" N PHE C 79 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 177 through 180 No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.488A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'D' and resid 13 through 15 No H-bonds generated for 'chain 'D' and resid 13 through 15' Processing helix chain 'D' and resid 25 through 51 Proline residue: D 35 - end of helix Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 71 through 96 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 108 through 130 Processing helix chain 'D' and resid 133 through 159 removed outlier: 3.761A pdb=" N ILE D 137 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA D 138 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 192 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 218 through 221 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.953A pdb=" N ALA D 235 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 240 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 328 removed outlier: 5.809A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 356 through 400 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.938A pdb=" N VAL D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 455 Proline residue: D 436 - end of helix Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 458 through 504 removed outlier: 3.903A pdb=" N LEU D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.579A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 511 Processing helix chain 'D' and resid 515 through 561 Proline residue: D 551 - end of helix Processing helix chain 'D' and resid 573 through 614 Proline residue: D 589 - end of helix removed outlier: 4.509A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 726 Processing helix chain 'D' and resid 784 through 789 Processing helix chain 'D' and resid 796 through 806 removed outlier: 3.559A pdb=" N MET D 801 " --> pdb=" O GLN D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 812 No H-bonds generated for 'chain 'D' and resid 809 through 812' Processing helix chain 'D' and resid 832 through 845 Processing helix chain 'D' and resid 862 through 871 Processing helix chain 'D' and resid 891 through 896 Proline residue: D 895 - end of helix Processing helix chain 'D' and resid 914 through 917 No H-bonds generated for 'chain 'D' and resid 914 through 917' Processing helix chain 'D' and resid 922 through 931 Processing helix chain 'D' and resid 1003 through 1008 Processing helix chain 'D' and resid 1010 through 1038 Processing helix chain 'D' and resid 1061 through 1106 removed outlier: 3.750A pdb=" N GLU D1087 " --> pdb=" O SER D1083 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS D1098 " --> pdb=" O ALA D1094 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D1106 " --> pdb=" O LEU D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1118 through 1126 removed outlier: 4.023A pdb=" N ARG D1124 " --> pdb=" O SER D1120 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1128 through 1160 removed outlier: 4.564A pdb=" N ILE D1136 " --> pdb=" O ILE D1132 " (cutoff:3.500A) Proline residue: D1137 - end of helix removed outlier: 3.552A pdb=" N GLU D1141 " --> pdb=" O PRO D1137 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D1151 " --> pdb=" O THR D1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 1162 through 1209 removed outlier: 3.773A pdb=" N LEU D1169 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 4.045A pdb=" N CYS D1175 " --> pdb=" O ALA D1172 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE D1182 " --> pdb=" O GLN D1179 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG D1183 " --> pdb=" O LYS D1180 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL D1184 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER D1186 " --> pdb=" O ARG D1183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D1187 " --> pdb=" O VAL D1184 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN D1190 " --> pdb=" O ARG D1187 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D1192 " --> pdb=" O LEU D1189 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR D1195 " --> pdb=" O LEU D1192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR D1196 " --> pdb=" O ASP D1193 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU D1198 " --> pdb=" O THR D1195 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 4.204A pdb=" N SER D1202 " --> pdb=" O PRO D1199 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU D1206 " --> pdb=" O HIS D1203 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D1208 " --> pdb=" O ALA D1205 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU D1209 " --> pdb=" O GLU D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1220 through 1273 Processing helix chain 'D' and resid 1280 through 1319 removed outlier: 3.582A pdb=" N MET D1290 " --> pdb=" O THR D1286 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN D1296 " --> pdb=" O SER D1292 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP D1297 " --> pdb=" O ASN D1293 " (cutoff:3.500A) Processing helix chain 'D' and resid 1385 through 1393 removed outlier: 3.652A pdb=" N SER D1389 " --> pdb=" O LYS D1385 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D1392 " --> pdb=" O PHE D1388 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE D1393 " --> pdb=" O SER D1389 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1412 No H-bonds generated for 'chain 'D' and resid 1410 through 1412' Processing helix chain 'D' and resid 1415 through 1420 Processing helix chain 'D' and resid 1436 through 1440 Processing helix chain 'D' and resid 1448 through 1457 Processing helix chain 'D' and resid 1461 through 1466 Processing helix chain 'D' and resid 1470 through 1472 No H-bonds generated for 'chain 'D' and resid 1470 through 1472' Processing helix chain 'D' and resid 1484 through 1496 Processing helix chain 'D' and resid 1508 through 1510 No H-bonds generated for 'chain 'D' and resid 1508 through 1510' Processing helix chain 'D' and resid 1514 through 1527 removed outlier: 3.652A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1540 through 1543 Processing helix chain 'D' and resid 1563 through 1566 No H-bonds generated for 'chain 'D' and resid 1563 through 1566' Processing helix chain 'D' and resid 1573 through 1579 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 68 through 96 removed outlier: 3.812A pdb=" N PHE E 79 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 143 through 171 Processing helix chain 'E' and resid 177 through 180 No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 266 through 269 removed outlier: 4.488A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 269' Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 25 through 51 Proline residue: F 35 - end of helix Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 71 through 96 Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 108 through 130 Processing helix chain 'F' and resid 133 through 159 removed outlier: 3.761A pdb=" N ILE F 137 " --> pdb=" O LYS F 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 138 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 192 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 218 through 221 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 231 through 242 removed outlier: 3.953A pdb=" N ALA F 235 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA F 240 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 328 removed outlier: 5.809A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE F 314 " --> pdb=" O ASP F 310 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 348 through 353 Processing helix chain 'F' and resid 356 through 400 Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.938A pdb=" N VAL F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 455 Proline residue: F 436 - end of helix Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 458 through 504 removed outlier: 3.903A pdb=" N LEU F 470 " --> pdb=" O VAL F 466 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.579A pdb=" N GLU F 494 " --> pdb=" O GLU F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 515 through 561 Proline residue: F 551 - end of helix Processing helix chain 'F' and resid 573 through 614 Proline residue: F 589 - end of helix removed outlier: 4.509A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 726 Processing helix chain 'F' and resid 784 through 789 Processing helix chain 'F' and resid 796 through 806 removed outlier: 3.559A pdb=" N MET F 801 " --> pdb=" O GLN F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 812 No H-bonds generated for 'chain 'F' and resid 809 through 812' Processing helix chain 'F' and resid 832 through 845 Processing helix chain 'F' and resid 862 through 871 Processing helix chain 'F' and resid 891 through 896 Proline residue: F 895 - end of helix Processing helix chain 'F' and resid 914 through 917 No H-bonds generated for 'chain 'F' and resid 914 through 917' Processing helix chain 'F' and resid 922 through 931 Processing helix chain 'F' and resid 1003 through 1008 Processing helix chain 'F' and resid 1010 through 1038 Processing helix chain 'F' and resid 1061 through 1106 removed outlier: 3.750A pdb=" N GLU F1087 " --> pdb=" O SER F1083 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS F1098 " --> pdb=" O ALA F1094 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE F1106 " --> pdb=" O LEU F1102 " (cutoff:3.500A) Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1126 removed outlier: 4.023A pdb=" N ARG F1124 " --> pdb=" O SER F1120 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1128 through 1160 removed outlier: 4.564A pdb=" N ILE F1136 " --> pdb=" O ILE F1132 " (cutoff:3.500A) Proline residue: F1137 - end of helix removed outlier: 3.552A pdb=" N GLU F1141 " --> pdb=" O PRO F1137 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL F1151 " --> pdb=" O THR F1147 " (cutoff:3.500A) Processing helix chain 'F' and resid 1162 through 1209 removed outlier: 3.773A pdb=" N LEU F1169 " --> pdb=" O VAL F1166 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 4.045A pdb=" N CYS F1175 " --> pdb=" O ALA F1172 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE F1182 " --> pdb=" O GLN F1179 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F1183 " --> pdb=" O LYS F1180 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL F1184 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER F1186 " --> pdb=" O ARG F1183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG F1187 " --> pdb=" O VAL F1184 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN F1190 " --> pdb=" O ARG F1187 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F1192 " --> pdb=" O LEU F1189 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR F1195 " --> pdb=" O LEU F1192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR F1196 " --> pdb=" O ASP F1193 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU F1198 " --> pdb=" O THR F1195 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 4.204A pdb=" N SER F1202 " --> pdb=" O PRO F1199 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU F1206 " --> pdb=" O HIS F1203 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL F1208 " --> pdb=" O ALA F1205 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU F1209 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1211 through 1216 Processing helix chain 'F' and resid 1220 through 1273 Processing helix chain 'F' and resid 1280 through 1319 removed outlier: 3.582A pdb=" N MET F1290 " --> pdb=" O THR F1286 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN F1296 " --> pdb=" O SER F1292 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP F1297 " --> pdb=" O ASN F1293 " (cutoff:3.500A) Processing helix chain 'F' and resid 1385 through 1393 removed outlier: 3.652A pdb=" N SER F1389 " --> pdb=" O LYS F1385 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE F1392 " --> pdb=" O PHE F1388 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE F1393 " --> pdb=" O SER F1389 " (cutoff:3.500A) Processing helix chain 'F' and resid 1410 through 1412 No H-bonds generated for 'chain 'F' and resid 1410 through 1412' Processing helix chain 'F' and resid 1415 through 1420 Processing helix chain 'F' and resid 1436 through 1440 Processing helix chain 'F' and resid 1448 through 1457 Processing helix chain 'F' and resid 1461 through 1466 Processing helix chain 'F' and resid 1470 through 1472 No H-bonds generated for 'chain 'F' and resid 1470 through 1472' Processing helix chain 'F' and resid 1484 through 1496 Processing helix chain 'F' and resid 1508 through 1510 No H-bonds generated for 'chain 'F' and resid 1508 through 1510' Processing helix chain 'F' and resid 1514 through 1527 removed outlier: 3.652A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1540 through 1543 Processing helix chain 'F' and resid 1563 through 1566 No H-bonds generated for 'chain 'F' and resid 1563 through 1566' Processing helix chain 'F' and resid 1573 through 1579 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 59 through 64 Processing helix chain 'G' and resid 68 through 96 removed outlier: 3.812A pdb=" N PHE G 79 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 143 through 171 Processing helix chain 'G' and resid 177 through 180 No H-bonds generated for 'chain 'G' and resid 177 through 180' Processing helix chain 'G' and resid 266 through 269 removed outlier: 4.488A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 269' Processing helix chain 'G' and resid 330 through 332 No H-bonds generated for 'chain 'G' and resid 330 through 332' Processing helix chain 'G' and resid 346 through 355 Processing helix chain 'H' and resid 13 through 15 No H-bonds generated for 'chain 'H' and resid 13 through 15' Processing helix chain 'H' and resid 25 through 51 Proline residue: H 35 - end of helix Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 71 through 96 Processing helix chain 'H' and resid 104 through 106 No H-bonds generated for 'chain 'H' and resid 104 through 106' Processing helix chain 'H' and resid 108 through 130 Processing helix chain 'H' and resid 133 through 159 removed outlier: 3.761A pdb=" N ILE H 137 " --> pdb=" O LYS H 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA H 138 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 192 Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 218 through 221 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 231 through 242 removed outlier: 3.953A pdb=" N ALA H 235 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA H 240 " --> pdb=" O ILE H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 328 removed outlier: 5.809A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE H 314 " --> pdb=" O ASP H 310 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 348 through 353 Processing helix chain 'H' and resid 356 through 400 Processing helix chain 'H' and resid 404 through 408 Processing helix chain 'H' and resid 414 through 422 removed outlier: 3.938A pdb=" N VAL H 421 " --> pdb=" O ILE H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 455 Proline residue: H 436 - end of helix Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 458 through 504 removed outlier: 3.903A pdb=" N LEU H 470 " --> pdb=" O VAL H 466 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.579A pdb=" N GLU H 494 " --> pdb=" O GLU H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 506 through 511 Processing helix chain 'H' and resid 515 through 561 Proline residue: H 551 - end of helix Processing helix chain 'H' and resid 573 through 614 Proline residue: H 589 - end of helix removed outlier: 4.509A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 726 Processing helix chain 'H' and resid 784 through 789 Processing helix chain 'H' and resid 796 through 806 removed outlier: 3.559A pdb=" N MET H 801 " --> pdb=" O GLN H 797 " (cutoff:3.500A) Processing helix chain 'H' and resid 809 through 812 No H-bonds generated for 'chain 'H' and resid 809 through 812' Processing helix chain 'H' and resid 832 through 845 Processing helix chain 'H' and resid 862 through 871 Processing helix chain 'H' and resid 891 through 896 Proline residue: H 895 - end of helix Processing helix chain 'H' and resid 914 through 917 No H-bonds generated for 'chain 'H' and resid 914 through 917' Processing helix chain 'H' and resid 922 through 931 Processing helix chain 'H' and resid 1003 through 1008 Processing helix chain 'H' and resid 1010 through 1038 Processing helix chain 'H' and resid 1061 through 1106 removed outlier: 3.750A pdb=" N GLU H1087 " --> pdb=" O SER H1083 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS H1098 " --> pdb=" O ALA H1094 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE H1106 " --> pdb=" O LEU H1102 " (cutoff:3.500A) Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1126 removed outlier: 4.023A pdb=" N ARG H1124 " --> pdb=" O SER H1120 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1128 through 1160 removed outlier: 4.564A pdb=" N ILE H1136 " --> pdb=" O ILE H1132 " (cutoff:3.500A) Proline residue: H1137 - end of helix removed outlier: 3.552A pdb=" N GLU H1141 " --> pdb=" O PRO H1137 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL H1151 " --> pdb=" O THR H1147 " (cutoff:3.500A) Processing helix chain 'H' and resid 1162 through 1209 removed outlier: 3.773A pdb=" N LEU H1169 " --> pdb=" O VAL H1166 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 4.045A pdb=" N CYS H1175 " --> pdb=" O ALA H1172 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE H1182 " --> pdb=" O GLN H1179 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG H1183 " --> pdb=" O LYS H1180 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL H1184 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER H1186 " --> pdb=" O ARG H1183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG H1187 " --> pdb=" O VAL H1184 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN H1190 " --> pdb=" O ARG H1187 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU H1192 " --> pdb=" O LEU H1189 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR H1195 " --> pdb=" O LEU H1192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR H1196 " --> pdb=" O ASP H1193 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU H1198 " --> pdb=" O THR H1195 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 4.204A pdb=" N SER H1202 " --> pdb=" O PRO H1199 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU H1206 " --> pdb=" O HIS H1203 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL H1208 " --> pdb=" O ALA H1205 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU H1209 " --> pdb=" O GLU H1206 " (cutoff:3.500A) Processing helix chain 'H' and resid 1211 through 1216 Processing helix chain 'H' and resid 1220 through 1273 Processing helix chain 'H' and resid 1280 through 1319 removed outlier: 3.582A pdb=" N MET H1290 " --> pdb=" O THR H1286 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN H1296 " --> pdb=" O SER H1292 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP H1297 " --> pdb=" O ASN H1293 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1393 removed outlier: 3.652A pdb=" N SER H1389 " --> pdb=" O LYS H1385 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE H1392 " --> pdb=" O PHE H1388 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE H1393 " --> pdb=" O SER H1389 " (cutoff:3.500A) Processing helix chain 'H' and resid 1410 through 1412 No H-bonds generated for 'chain 'H' and resid 1410 through 1412' Processing helix chain 'H' and resid 1415 through 1420 Processing helix chain 'H' and resid 1436 through 1440 Processing helix chain 'H' and resid 1448 through 1457 Processing helix chain 'H' and resid 1461 through 1466 Processing helix chain 'H' and resid 1470 through 1472 No H-bonds generated for 'chain 'H' and resid 1470 through 1472' Processing helix chain 'H' and resid 1484 through 1496 Processing helix chain 'H' and resid 1508 through 1510 No H-bonds generated for 'chain 'H' and resid 1508 through 1510' Processing helix chain 'H' and resid 1514 through 1527 removed outlier: 3.652A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1540 through 1543 Processing helix chain 'H' and resid 1563 through 1566 No H-bonds generated for 'chain 'H' and resid 1563 through 1566' Processing helix chain 'H' and resid 1573 through 1579 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.850A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.398A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= F, first strand: chain 'B' and resid 736 through 739 removed outlier: 6.923A pdb=" N ILE B 703 " --> pdb=" O CYS B 678 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN B 680 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 701 " --> pdb=" O GLN B 680 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 908 through 912 removed outlier: 6.922A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 884 " --> pdb=" O THR B 709 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 711 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 886 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY B 713 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1367 through 1369 Processing sheet with id= I, first strand: chain 'B' and resid 1556 through 1561 removed outlier: 6.753A pdb=" N VAL B1551 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B1560 " --> pdb=" O VAL B1549 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B1549 " --> pdb=" O PHE B1560 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B1533 " --> pdb=" O ILE B1375 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE B1377 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B1535 " --> pdb=" O ILE B1377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 685 through 687 removed outlier: 6.222A pdb=" N THR B 687 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS B 732 " --> pdb=" O THR B 687 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1351 through 1353 removed outlier: 3.634A pdb=" N GLU B1400 " --> pdb=" O SER B1351 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARG B1353 " --> pdb=" O MET B1398 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= M, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.850A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.398A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= P, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= Q, first strand: chain 'D' and resid 736 through 739 removed outlier: 6.923A pdb=" N ILE D 703 " --> pdb=" O CYS D 678 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN D 680 " --> pdb=" O ILE D 701 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 701 " --> pdb=" O GLN D 680 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 908 through 912 removed outlier: 6.922A pdb=" N ALA D 902 " --> pdb=" O GLN D 909 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU D 911 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 900 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 884 " --> pdb=" O THR D 709 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE D 711 " --> pdb=" O VAL D 884 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 886 " --> pdb=" O ILE D 711 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY D 713 " --> pdb=" O LEU D 886 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 1367 through 1369 Processing sheet with id= T, first strand: chain 'D' and resid 1556 through 1561 removed outlier: 6.753A pdb=" N VAL D1551 " --> pdb=" O LEU D1558 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D1560 " --> pdb=" O VAL D1549 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL D1549 " --> pdb=" O PHE D1560 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D1533 " --> pdb=" O ILE D1375 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE D1377 " --> pdb=" O VAL D1533 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D1535 " --> pdb=" O ILE D1377 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 685 through 687 removed outlier: 6.222A pdb=" N THR D 687 " --> pdb=" O LYS D 732 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS D 732 " --> pdb=" O THR D 687 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 1351 through 1353 removed outlier: 3.634A pdb=" N GLU D1400 " --> pdb=" O SER D1351 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARG D1353 " --> pdb=" O MET D1398 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET D1398 " --> pdb=" O ARG D1353 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= X, first strand: chain 'E' and resid 309 through 311 removed outlier: 6.850A pdb=" N ALA E 187 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 234 through 238 removed outlier: 4.398A pdb=" N MET E 217 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= AA, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= AB, first strand: chain 'F' and resid 736 through 739 removed outlier: 6.923A pdb=" N ILE F 703 " --> pdb=" O CYS F 678 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN F 680 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE F 701 " --> pdb=" O GLN F 680 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 908 through 912 removed outlier: 6.922A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL F 884 " --> pdb=" O THR F 709 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE F 711 " --> pdb=" O VAL F 884 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU F 886 " --> pdb=" O ILE F 711 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY F 713 " --> pdb=" O LEU F 886 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 1367 through 1369 Processing sheet with id= AE, first strand: chain 'F' and resid 1556 through 1561 removed outlier: 6.753A pdb=" N VAL F1551 " --> pdb=" O LEU F1558 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F1560 " --> pdb=" O VAL F1549 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL F1549 " --> pdb=" O PHE F1560 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL F1533 " --> pdb=" O ILE F1375 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE F1377 " --> pdb=" O VAL F1533 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR F1535 " --> pdb=" O ILE F1377 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 685 through 687 removed outlier: 6.222A pdb=" N THR F 687 " --> pdb=" O LYS F 732 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS F 732 " --> pdb=" O THR F 687 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 1351 through 1353 removed outlier: 3.634A pdb=" N GLU F1400 " --> pdb=" O SER F1351 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARG F1353 " --> pdb=" O MET F1398 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET F1398 " --> pdb=" O ARG F1353 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= AI, first strand: chain 'G' and resid 309 through 311 removed outlier: 6.850A pdb=" N ALA G 187 " --> pdb=" O LEU G 310 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 234 through 238 removed outlier: 4.398A pdb=" N MET G 217 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 313 through 315 Processing sheet with id= AL, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= AM, first strand: chain 'H' and resid 736 through 739 removed outlier: 6.923A pdb=" N ILE H 703 " --> pdb=" O CYS H 678 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN H 680 " --> pdb=" O ILE H 701 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE H 701 " --> pdb=" O GLN H 680 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 908 through 912 removed outlier: 6.922A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL H 884 " --> pdb=" O THR H 709 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE H 711 " --> pdb=" O VAL H 884 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU H 886 " --> pdb=" O ILE H 711 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY H 713 " --> pdb=" O LEU H 886 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 1367 through 1369 Processing sheet with id= AP, first strand: chain 'H' and resid 1556 through 1561 removed outlier: 6.753A pdb=" N VAL H1551 " --> pdb=" O LEU H1558 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE H1560 " --> pdb=" O VAL H1549 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL H1549 " --> pdb=" O PHE H1560 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL H1533 " --> pdb=" O ILE H1375 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE H1377 " --> pdb=" O VAL H1533 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR H1535 " --> pdb=" O ILE H1377 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 685 through 687 removed outlier: 6.222A pdb=" N THR H 687 " --> pdb=" O LYS H 732 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS H 732 " --> pdb=" O THR H 687 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 1351 through 1353 removed outlier: 3.634A pdb=" N GLU H1400 " --> pdb=" O SER H1351 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARG H1353 " --> pdb=" O MET H1398 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET H1398 " --> pdb=" O ARG H1353 " (cutoff:3.500A) 3000 hydrogen bonds defined for protein. 8184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.08 Time building geometry restraints manager: 18.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8496 1.32 - 1.44: 14936 1.44 - 1.56: 31948 1.56 - 1.69: 48 1.69 - 1.81: 488 Bond restraints: 55916 Sorted by residual: bond pdb=" C13 E2H H1604 " pdb=" N07 E2H H1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C13 E2H F1604 " pdb=" N07 E2H F1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C13 E2H D1604 " pdb=" N07 E2H D1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C13 E2H B1604 " pdb=" N07 E2H B1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C14 E2H H1604 " pdb=" N07 E2H H1604 " ideal model delta sigma weight residual 1.371 1.554 -0.183 2.00e-02 2.50e+03 8.37e+01 ... (remaining 55911 not shown) Histogram of bond angle deviations from ideal: 59.76 - 75.77: 12 75.77 - 91.79: 0 91.79 - 107.81: 2192 107.81 - 123.83: 72116 123.83 - 139.84: 1652 Bond angle restraints: 75972 Sorted by residual: angle pdb=" C GLY D 353 " pdb=" N ASN D 354 " pdb=" CA ASN D 354 " ideal model delta sigma weight residual 121.54 133.57 -12.03 1.91e+00 2.74e-01 3.97e+01 angle pdb=" C GLY B 353 " pdb=" N ASN B 354 " pdb=" CA ASN B 354 " ideal model delta sigma weight residual 121.54 133.57 -12.03 1.91e+00 2.74e-01 3.97e+01 angle pdb=" C GLY H 353 " pdb=" N ASN H 354 " pdb=" CA ASN H 354 " ideal model delta sigma weight residual 121.54 133.57 -12.03 1.91e+00 2.74e-01 3.97e+01 angle pdb=" C GLY F 353 " pdb=" N ASN F 354 " pdb=" CA ASN F 354 " ideal model delta sigma weight residual 121.54 133.57 -12.03 1.91e+00 2.74e-01 3.97e+01 angle pdb=" C15 E2H B1604 " pdb=" S03 E2H B1604 " pdb=" C17 E2H B1604 " ideal model delta sigma weight residual 90.00 107.64 -17.64 3.00e+00 1.11e-01 3.46e+01 ... (remaining 75967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 32028 23.63 - 47.26: 1008 47.26 - 70.88: 112 70.88 - 94.51: 12 94.51 - 118.14: 8 Dihedral angle restraints: 33168 sinusoidal: 12988 harmonic: 20180 Sorted by residual: dihedral pdb=" O1B ADP H1601 " pdb=" O3A ADP H1601 " pdb=" PB ADP H1601 " pdb=" PA ADP H1601 " ideal model delta sinusoidal sigma weight residual -60.00 -178.14 118.14 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" O1B ADP B1601 " pdb=" O3A ADP B1601 " pdb=" PB ADP B1601 " pdb=" PA ADP B1601 " ideal model delta sinusoidal sigma weight residual -60.00 -178.14 118.14 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" O1B ADP D1601 " pdb=" O3A ADP D1601 " pdb=" PB ADP D1601 " pdb=" PA ADP D1601 " ideal model delta sinusoidal sigma weight residual -60.00 -178.14 118.14 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 33165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 7932 0.070 - 0.140: 1012 0.140 - 0.210: 72 0.210 - 0.279: 0 0.279 - 0.349: 4 Chirality restraints: 9020 Sorted by residual: chirality pdb=" CG LEU D1227 " pdb=" CB LEU D1227 " pdb=" CD1 LEU D1227 " pdb=" CD2 LEU D1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CG LEU F1227 " pdb=" CB LEU F1227 " pdb=" CD1 LEU F1227 " pdb=" CD2 LEU F1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CG LEU B1227 " pdb=" CB LEU B1227 " pdb=" CD1 LEU B1227 " pdb=" CD2 LEU B1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 9017 not shown) Planarity restraints: 9360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 147 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C PHE D 147 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE D 147 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE D 148 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 147 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C PHE B 147 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE B 147 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE B 148 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 147 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C PHE F 147 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE F 147 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE F 148 " -0.020 2.00e-02 2.50e+03 ... (remaining 9357 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1232 2.70 - 3.25: 52808 3.25 - 3.80: 91256 3.80 - 4.35: 119718 4.35 - 4.90: 199312 Nonbonded interactions: 464326 Sorted by model distance: nonbonded pdb=" OE1 GLN H 775 " pdb="MG MG H1602 " model vdw 2.150 2.170 nonbonded pdb=" OE1 GLN F 775 " pdb="MG MG F1602 " model vdw 2.150 2.170 nonbonded pdb=" OE1 GLN D 775 " pdb="MG MG D1602 " model vdw 2.150 2.170 nonbonded pdb=" OE1 GLN B 775 " pdb="MG MG B1602 " model vdw 2.150 2.170 nonbonded pdb=" O PRO H 793 " pdb=" OH TYR H 845 " model vdw 2.221 2.440 ... (remaining 464321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.640 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 107.870 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.300 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:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.006 0.205 55916 Z= 0.361 Angle : 0.743 17.639 75972 Z= 0.400 Chirality : 0.046 0.349 9020 Planarity : 0.006 0.056 9360 Dihedral : 11.823 118.138 20040 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.91 % Favored : 96.97 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.09), residues: 6872 helix: 0.28 (0.07), residues: 4116 sheet: -0.60 (0.21), residues: 524 loop : -0.38 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1134 time to evaluate : 5.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 22 residues processed: 1238 average time/residue: 1.3771 time to fit residues: 2152.4404 Evaluate side-chains 751 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 729 time to evaluate : 4.798 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 8 average time/residue: 0.7678 time to fit residues: 15.3872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 584 optimal weight: 6.9990 chunk 524 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 353 optimal weight: 0.0070 chunk 280 optimal weight: 10.0000 chunk 542 optimal weight: 0.1980 chunk 209 optimal weight: 0.0980 chunk 329 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 628 optimal weight: 10.0000 overall best weight: 2.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 52 GLN B 72 ASN B 416 GLN B 444 GLN B 608 GLN B1541 HIS C 46 HIS C 52 GLN C 173 GLN C 348 GLN D 59 HIS D 339 GLN D 416 GLN D1541 HIS E 46 HIS E 52 GLN E 173 GLN E 348 GLN F 59 HIS F 72 ASN F 416 GLN F1541 HIS G 46 HIS G 52 GLN G 107 ASN G 173 GLN G 299 GLN H 72 ASN H 416 GLN H 444 GLN H 608 GLN H1541 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 55916 Z= 0.192 Angle : 0.507 9.301 75972 Z= 0.258 Chirality : 0.040 0.203 9020 Planarity : 0.004 0.048 9360 Dihedral : 5.591 106.724 7524 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.10 % Favored : 97.79 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.10), residues: 6872 helix: 1.31 (0.08), residues: 4152 sheet: -0.32 (0.22), residues: 476 loop : -0.22 (0.13), residues: 2244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 796 time to evaluate : 5.098 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 214 outliers final: 74 residues processed: 926 average time/residue: 1.3176 time to fit residues: 1558.8999 Evaluate side-chains 782 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 708 time to evaluate : 4.807 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 54 residues processed: 21 average time/residue: 0.7058 time to fit residues: 28.7518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 349 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 523 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 629 optimal weight: 8.9990 chunk 680 optimal weight: 6.9990 chunk 560 optimal weight: 9.9990 chunk 624 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 505 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 474 GLN B 562 HIS B1123 ASN B1134 GLN B1203 HIS B1541 HIS C 173 GLN D 103 HIS D 397 ASN D 474 GLN D 562 HIS D1134 GLN D1203 HIS D1224 GLN E 52 GLN E 218 GLN F 59 HIS F 397 ASN F 474 GLN F 562 HIS F1123 ASN F1134 GLN F1203 HIS F1224 GLN F1521 GLN F1541 HIS G 218 GLN G 235 GLN H 397 ASN H 416 GLN H 474 GLN H 562 HIS H1123 ASN H1134 GLN H1203 HIS H1224 GLN H1225 GLN H1541 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 55916 Z= 0.420 Angle : 0.604 7.871 75972 Z= 0.304 Chirality : 0.044 0.155 9020 Planarity : 0.004 0.044 9360 Dihedral : 5.856 104.075 7524 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.43 % Favored : 97.40 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.10), residues: 6872 helix: 1.35 (0.08), residues: 4156 sheet: -0.64 (0.21), residues: 524 loop : -0.26 (0.13), residues: 2192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 727 time to evaluate : 5.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 290 outliers final: 139 residues processed: 912 average time/residue: 1.3829 time to fit residues: 1597.6891 Evaluate side-chains 816 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 677 time to evaluate : 4.854 Switching outliers to nearest non-outliers outliers start: 139 outliers final: 108 residues processed: 32 average time/residue: 1.0213 time to fit residues: 50.6962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 621 optimal weight: 5.9990 chunk 473 optimal weight: 3.9990 chunk 326 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 300 optimal weight: 5.9990 chunk 422 optimal weight: 0.2980 chunk 631 optimal weight: 0.8980 chunk 668 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 598 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN B1123 ASN B1541 HIS ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D1224 GLN E 107 ASN E 173 GLN E 348 GLN F 59 HIS F1123 ASN F1224 GLN F1541 HIS H 416 GLN H1123 ASN H1224 GLN H1225 GLN H1541 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 55916 Z= 0.171 Angle : 0.494 9.166 75972 Z= 0.249 Chirality : 0.039 0.138 9020 Planarity : 0.004 0.054 9360 Dihedral : 5.617 105.706 7524 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.12 % Favored : 97.70 % Rotamer Outliers : 4.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 6872 helix: 1.79 (0.08), residues: 4092 sheet: -0.77 (0.21), residues: 544 loop : -0.14 (0.13), residues: 2236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 708 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 244 outliers final: 114 residues processed: 885 average time/residue: 1.3877 time to fit residues: 1560.0380 Evaluate side-chains 790 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 676 time to evaluate : 4.816 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 97 residues processed: 18 average time/residue: 0.9545 time to fit residues: 30.1468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 557 optimal weight: 20.0000 chunk 379 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 498 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 570 optimal weight: 30.0000 chunk 462 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 600 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 397 ASN B1123 ASN ** B1270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1541 HIS C 173 GLN D 863 HIS ** D1270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN E 348 GLN F 59 HIS F 397 ASN F1123 ASN F1225 GLN F1541 HIS H 397 ASN H 416 GLN H1123 ASN H1541 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.084 55916 Z= 0.563 Angle : 0.679 9.799 75972 Z= 0.339 Chirality : 0.047 0.196 9020 Planarity : 0.005 0.050 9360 Dihedral : 5.868 110.721 7524 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.98 % Favored : 96.84 % Rotamer Outliers : 4.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 6872 helix: 1.36 (0.08), residues: 4104 sheet: -0.79 (0.22), residues: 512 loop : -0.34 (0.13), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 706 time to evaluate : 5.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 282 outliers final: 160 residues processed: 885 average time/residue: 1.4078 time to fit residues: 1578.8249 Evaluate side-chains 829 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 669 time to evaluate : 4.839 Switching outliers to nearest non-outliers outliers start: 160 outliers final: 116 residues processed: 45 average time/residue: 0.9481 time to fit residues: 65.6505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 225 optimal weight: 0.9980 chunk 602 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 392 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 669 optimal weight: 5.9990 chunk 555 optimal weight: 0.9990 chunk 309 optimal weight: 0.7980 chunk 55 optimal weight: 0.0030 chunk 221 optimal weight: 9.9990 chunk 351 optimal weight: 0.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN B1123 ASN B1541 HIS C 299 GLN D 397 ASN E 216 HIS E 348 GLN F 59 HIS F 397 ASN F1123 ASN F1541 HIS H 293 HIS H 397 ASN H 416 GLN H1123 ASN H1203 HIS H1541 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 55916 Z= 0.146 Angle : 0.503 9.209 75972 Z= 0.253 Chirality : 0.040 0.237 9020 Planarity : 0.004 0.058 9360 Dihedral : 5.473 110.678 7524 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.07 % Favored : 97.76 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.10), residues: 6872 helix: 1.87 (0.08), residues: 4096 sheet: -0.95 (0.21), residues: 548 loop : -0.21 (0.13), residues: 2228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 700 time to evaluate : 4.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 206 outliers final: 109 residues processed: 865 average time/residue: 1.4160 time to fit residues: 1548.4033 Evaluate side-chains 758 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 649 time to evaluate : 4.855 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 100 residues processed: 10 average time/residue: 0.9250 time to fit residues: 19.5528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 645 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 381 optimal weight: 8.9990 chunk 488 optimal weight: 8.9990 chunk 378 optimal weight: 10.0000 chunk 563 optimal weight: 8.9990 chunk 373 optimal weight: 3.9990 chunk 666 optimal weight: 7.9990 chunk 417 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 216 HIS B 19 GLN B 397 ASN B1123 ASN ** B1270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1541 HIS C 173 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN D 397 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN F 397 ASN F1123 ASN F1541 HIS H 397 ASN H 416 GLN H1123 ASN H1203 HIS H1541 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 55916 Z= 0.399 Angle : 0.594 11.058 75972 Z= 0.297 Chirality : 0.044 0.194 9020 Planarity : 0.004 0.054 9360 Dihedral : 5.577 110.992 7524 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.63 % Favored : 97.19 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.10), residues: 6872 helix: 1.68 (0.08), residues: 4108 sheet: -0.88 (0.22), residues: 512 loop : -0.25 (0.13), residues: 2252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 680 time to evaluate : 4.945 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 142 residues processed: 842 average time/residue: 1.4266 time to fit residues: 1521.8514 Evaluate side-chains 801 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 659 time to evaluate : 4.838 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 120 residues processed: 23 average time/residue: 1.1967 time to fit residues: 42.5510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 412 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 398 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 424 optimal weight: 3.9990 chunk 454 optimal weight: 3.9990 chunk 329 optimal weight: 0.0970 chunk 62 optimal weight: 5.9990 chunk 524 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 216 HIS B 293 HIS B 397 ASN B1123 ASN B1541 HIS D 293 HIS D 397 ASN D 444 GLN E 348 GLN F 397 ASN F1123 ASN F1541 HIS H 397 ASN H 416 GLN ** H 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1123 ASN H1541 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 55916 Z= 0.217 Angle : 0.532 10.483 75972 Z= 0.266 Chirality : 0.041 0.204 9020 Planarity : 0.004 0.053 9360 Dihedral : 5.455 112.133 7524 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.46 % Favored : 97.37 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.10), residues: 6872 helix: 1.83 (0.08), residues: 4104 sheet: -1.06 (0.21), residues: 532 loop : -0.20 (0.13), residues: 2236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 685 time to evaluate : 5.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 130 residues processed: 836 average time/residue: 1.4266 time to fit residues: 1509.9392 Evaluate side-chains 790 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 660 time to evaluate : 4.813 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 119 residues processed: 12 average time/residue: 0.6985 time to fit residues: 19.2976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 606 optimal weight: 20.0000 chunk 638 optimal weight: 10.0000 chunk 582 optimal weight: 10.0000 chunk 621 optimal weight: 0.0870 chunk 374 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 488 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 561 optimal weight: 0.8980 chunk 587 optimal weight: 4.9990 chunk 619 optimal weight: 5.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 107 ASN A 216 HIS B 19 GLN B1123 ASN B1541 HIS D 397 ASN E 107 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN F 444 GLN F 863 HIS F1123 ASN F1541 HIS H1123 ASN H1541 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 55916 Z= 0.274 Angle : 0.553 10.785 75972 Z= 0.277 Chirality : 0.042 0.193 9020 Planarity : 0.004 0.055 9360 Dihedral : 5.436 111.960 7524 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.63 % Favored : 97.19 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.10), residues: 6872 helix: 1.78 (0.08), residues: 4108 sheet: -1.11 (0.21), residues: 552 loop : -0.19 (0.13), residues: 2212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 677 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 135 residues processed: 826 average time/residue: 1.4285 time to fit residues: 1495.1438 Evaluate side-chains 780 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 645 time to evaluate : 4.827 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 118 residues processed: 18 average time/residue: 1.0114 time to fit residues: 31.2928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 408 optimal weight: 10.0000 chunk 657 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 456 optimal weight: 4.9990 chunk 689 optimal weight: 3.9990 chunk 634 optimal weight: 0.9990 chunk 548 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 424 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 216 HIS ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN B1541 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1123 ASN F1541 HIS H 863 HIS H1123 ASN ** H1225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1541 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 55916 Z= 0.331 Angle : 0.593 12.165 75972 Z= 0.294 Chirality : 0.043 0.382 9020 Planarity : 0.004 0.058 9360 Dihedral : 5.458 113.670 7524 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.78 % Favored : 97.05 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 6872 helix: 1.70 (0.08), residues: 4100 sheet: -1.14 (0.21), residues: 552 loop : -0.27 (0.13), residues: 2220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13744 Ramachandran restraints generated. 6872 Oldfield, 0 Emsley, 6872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 665 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 136 residues processed: 803 average time/residue: 1.4649 time to fit residues: 1486.7885 Evaluate side-chains 794 residues out of total 6032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 658 time to evaluate : 4.820 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 121 residues processed: 16 average time/residue: 0.7794 time to fit residues: 24.8893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 436 optimal weight: 8.9990 chunk 584 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 506 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 549 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 564 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 216 HIS ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 ASN B1541 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 348 GLN F1123 ASN F1541 HIS H 188 ASN H1123 ASN ** H1225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1541 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083922 restraints weight = 108027.060| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.03 r_work: 0.3104 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 55916 Z= 0.306 Angle : 0.575 13.846 75972 Z= 0.287 Chirality : 0.042 0.335 9020 Planarity : 0.004 0.058 9360 Dihedral : 5.375 116.657 7524 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.71 % Favored : 97.12 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 6872 helix: 1.68 (0.08), residues: 4104 sheet: -1.17 (0.21), residues: 552 loop : -0.27 (0.13), residues: 2216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20995.65 seconds wall clock time: 364 minutes 48.02 seconds (21888.02 seconds total)