Starting phenix.real_space_refine on Mon Jul 6 23:44:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.cif" model { file = "/net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oop_17025/07_2026/8oop_17025.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.324 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 234 5.49 5 Mg 2 5.21 5 S 160 5.16 5 C 24886 2.51 5 N 7340 2.21 5 O 8120 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40747 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3401 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3414 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "F" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3394 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain breaks: 1 Chain: "G" Number of atoms: 5736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5736 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 670} Chain breaks: 2 Chain: "H" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 283 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4472 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 601} Chain breaks: 5 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 807 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLU:plan': 32, 'ARG:plan': 28, 'GLN:plan1': 11, 'TYR:plan': 4, 'ASP:plan': 12, 'ASN:plan1': 5, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 415 Chain: "K" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2243 Classifications: {'DNA': 110} Link IDs: {'rna3p': 109} Chain: "L" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2201 Classifications: {'DNA': 107} Link IDs: {'rna3p': 106} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.43, per 1000 atoms: 0.21 Number of scatterers: 40747 At special positions: 0 Unit cell: (134.808, 180.018, 192.348, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 160 16.00 P 234 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 8120 8.00 N 7340 7.00 C 24886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 40 sheets defined 51.3% alpha, 11.2% beta 61 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'A' and resid 76 through 89 Processing helix chain 'A' and resid 100 through 103 removed outlier: 3.875A pdb=" N TYR A 103 " --> pdb=" O SER A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.697A pdb=" N VAL A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.667A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.653A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 453 through 454 No H-bonds generated for 'chain 'A' and resid 453 through 454' Processing helix chain 'A' and resid 455 through 459 removed outlier: 4.065A pdb=" N HIS A 458 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 459 " --> pdb=" O GLY A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 459' Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.760A pdb=" N TYR B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.536A pdb=" N ARG B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 removed outlier: 4.625A pdb=" N ILE B 257 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE B 258 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN B 263 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 264 " --> pdb=" O MET B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.662A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.580A pdb=" N HIS B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.759A pdb=" N GLN B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 427 through 438 Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.745A pdb=" N HIS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 100 through 103 removed outlier: 3.548A pdb=" N TYR C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 273 through 290 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.847A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 410 through 420 Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.973A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.522A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.660A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.506A pdb=" N GLY D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.654A pdb=" N ARG D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 304 through 315 removed outlier: 4.179A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 382 through 397 Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.870A pdb=" N THR D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 106 through 109 removed outlier: 3.660A pdb=" N PHE E 109 " --> pdb=" O SER E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 114 through 126 removed outlier: 3.607A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 208 through 214 removed outlier: 5.705A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.619A pdb=" N ARG E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 Processing helix chain 'E' and resid 304 through 315 removed outlier: 4.180A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 362 through 377 Processing helix chain 'E' and resid 382 through 397 Processing helix chain 'E' and resid 397 through 415 removed outlier: 4.081A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.509A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 174 through 184 Processing helix chain 'F' and resid 209 through 214 removed outlier: 4.376A pdb=" N ARG F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR F 214 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 removed outlier: 4.252A pdb=" N ARG F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.723A pdb=" N ARG F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 304 through 316 removed outlier: 3.818A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU F 316 " --> pdb=" O ASN F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 362 through 377 Processing helix chain 'F' and resid 382 through 397 Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.121A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'G' and resid 965 through 969 Processing helix chain 'G' and resid 973 through 989 removed outlier: 3.729A pdb=" N GLY G 979 " --> pdb=" O TYR G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 1002 through 1019 removed outlier: 3.543A pdb=" N ILE G1008 " --> pdb=" O THR G1004 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET G1011 " --> pdb=" O SER G1007 " (cutoff:3.500A) Processing helix chain 'G' and resid 1029 through 1031 No H-bonds generated for 'chain 'G' and resid 1029 through 1031' Processing helix chain 'G' and resid 1032 through 1044 Processing helix chain 'G' and resid 1055 through 1063 Processing helix chain 'G' and resid 1064 through 1066 No H-bonds generated for 'chain 'G' and resid 1064 through 1066' Processing helix chain 'G' and resid 1087 through 1092 Processing helix chain 'G' and resid 1092 through 1097 Processing helix chain 'G' and resid 1108 through 1112 Processing helix chain 'G' and resid 1117 through 1125 removed outlier: 3.674A pdb=" N LEU G1123 " --> pdb=" O ARG G1119 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY G1125 " --> pdb=" O LYS G1121 " (cutoff:3.500A) Processing helix chain 'G' and resid 1143 through 1154 removed outlier: 4.480A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1186 through 1188 No H-bonds generated for 'chain 'G' and resid 1186 through 1188' Processing helix chain 'G' and resid 1189 through 1194 removed outlier: 3.594A pdb=" N ILE G1193 " --> pdb=" O ARG G1189 " (cutoff:3.500A) Processing helix chain 'G' and resid 1223 through 1240 removed outlier: 3.517A pdb=" N SER G1232 " --> pdb=" O ALA G1228 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G1238 " --> pdb=" O ARG G1234 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1270 removed outlier: 4.979A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL G1267 " --> pdb=" O GLN G1263 " (cutoff:3.500A) Processing helix chain 'G' and resid 1270 through 1275 removed outlier: 3.976A pdb=" N PHE G1274 " --> pdb=" O HIS G1270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1294 through 1298 removed outlier: 3.509A pdb=" N GLU G1297 " --> pdb=" O PHE G1294 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY G1298 " --> pdb=" O LEU G1295 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1294 through 1298' Processing helix chain 'G' and resid 1316 through 1321 Processing helix chain 'G' and resid 1333 through 1345 removed outlier: 4.398A pdb=" N GLY G1337 " --> pdb=" O ASN G1333 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1351 through 1356 Processing helix chain 'G' and resid 1365 through 1371 removed outlier: 3.735A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL G1371 " --> pdb=" O LEU G1368 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1384 removed outlier: 3.516A pdb=" N HIS G1383 " --> pdb=" O TYR G1379 " (cutoff:3.500A) Processing helix chain 'G' and resid 1385 through 1393 Processing helix chain 'G' and resid 1394 through 1396 No H-bonds generated for 'chain 'G' and resid 1394 through 1396' Processing helix chain 'G' and resid 1398 through 1407 removed outlier: 3.692A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1409 through 1413 Processing helix chain 'G' and resid 1417 through 1421 Processing helix chain 'G' and resid 1423 through 1428 Processing helix chain 'G' and resid 1429 through 1435 removed outlier: 4.474A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) Processing helix chain 'G' and resid 1440 through 1446 Processing helix chain 'G' and resid 1447 through 1456 Processing helix chain 'G' and resid 1480 through 1492 removed outlier: 3.575A pdb=" N VAL G1484 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 1493 through 1502 Processing helix chain 'G' and resid 1504 through 1514 removed outlier: 3.736A pdb=" N GLY G1514 " --> pdb=" O GLU G1510 " (cutoff:3.500A) Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1569 Processing helix chain 'G' and resid 1578 through 1591 removed outlier: 3.553A pdb=" N ILE G1582 " --> pdb=" O MET G1578 " (cutoff:3.500A) Processing helix chain 'G' and resid 1604 through 1618 Processing helix chain 'G' and resid 1628 through 1633 removed outlier: 4.468A pdb=" N LEU G1633 " --> pdb=" O ARG G1629 " (cutoff:3.500A) Processing helix chain 'G' and resid 1651 through 1663 removed outlier: 3.821A pdb=" N ASP G1655 " --> pdb=" O ASN G1651 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA G1662 " --> pdb=" O ALA G1658 " (cutoff:3.500A) Processing helix chain 'G' and resid 1682 through 1700 Processing helix chain 'H' and resid 468 through 475 removed outlier: 4.037A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 21 Processing helix chain 'I' and resid 43 through 49 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 203 through 212 removed outlier: 3.650A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 22 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.731A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 228 Processing helix chain 'J' and resid 234 through 250 Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.708A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 removed outlier: 3.940A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 Processing helix chain 'J' and resid 312 through 358 Processing helix chain 'J' and resid 361 through 373 Processing helix chain 'J' and resid 376 through 392 Processing helix chain 'J' and resid 430 through 469 Processing helix chain 'J' and resid 469 through 499 removed outlier: 4.204A pdb=" N LEU J 494 " --> pdb=" O GLU J 490 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP J 497 " --> pdb=" O ARG J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 589 Processing helix chain 'J' and resid 593 through 596 Processing helix chain 'J' and resid 597 through 603 Processing helix chain 'J' and resid 604 through 607 Processing helix chain 'J' and resid 608 through 615 Processing helix chain 'J' and resid 634 through 639 removed outlier: 3.686A pdb=" N VAL J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 651 Processing helix chain 'J' and resid 656 through 667 Processing helix chain 'J' and resid 679 through 684 Processing helix chain 'J' and resid 690 through 694 Processing helix chain 'J' and resid 697 through 708 removed outlier: 3.585A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 Processing helix chain 'J' and resid 738 through 745 Processing helix chain 'J' and resid 748 through 755 Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.612A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.528A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 30 through 40 Processing helix chain 'N' and resid 49 through 75 removed outlier: 3.596A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 92 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 90 Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 34 through 46 removed outlier: 3.843A pdb=" N GLN P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 82 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 119 Processing helix chain 'Q' and resid 44 through 55 removed outlier: 3.548A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 77 removed outlier: 3.532A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.583A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.592A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.669A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 60 " --> pdb=" O GLY R 56 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.540A pdb=" N VAL R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 98 removed outlier: 6.489A pdb=" N LEU A 300 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA A 331 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE A 302 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 144 removed outlier: 6.821A pdb=" N VAL A 136 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 162 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU A 138 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE A 160 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR A 140 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU A 158 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU A 142 " --> pdb=" O SER A 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 173 current: chain 'A' and resid 200 through 207 removed outlier: 6.012A pdb=" N VAL A 222 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG A 206 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 98 removed outlier: 6.325A pdb=" N CYS B 95 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 303 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 97 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 67 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N SER B 332 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 69 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 141 removed outlier: 5.995A pdb=" N GLY B 161 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 139 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 159 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 158 " --> pdb=" O LEU B 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 173 current: chain 'B' and resid 200 through 207 removed outlier: 6.336A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 339 removed outlier: 5.707A pdb=" N LEU B 345 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain 'C' and resid 94 through 98 removed outlier: 6.408A pdb=" N CYS C 95 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP C 303 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 97 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 67 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER C 332 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C 69 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 143 removed outlier: 6.140A pdb=" N GLY C 161 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET C 139 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 159 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 157 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 143 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE C 155 " --> pdb=" O GLU C 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 201 through 207 removed outlier: 6.633A pdb=" N VAL C 222 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 222 current: chain 'D' and resid 156 through 163 removed outlier: 3.536A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 168 through 173 current: chain 'D' and resid 201 through 206 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 201 through 206 current: chain 'H' and resid 456 through 461 Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 339 removed outlier: 5.901A pdb=" N LEU C 345 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 386 through 387 removed outlier: 6.715A pdb=" N GLN C 386 " --> pdb=" O VAL C 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.369A pdb=" N THR D 101 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP D 298 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 103 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.295A pdb=" N THR E 101 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASP E 298 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU E 103 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 148 removed outlier: 5.374A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 157 " --> pdb=" O ASP E 148 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY E 158 " --> pdb=" O MET E 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 168 through 173 current: chain 'E' and resid 201 through 206 Processing sheet with id=AC2, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.575A pdb=" N THR F 101 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP F 298 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU F 103 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU F 295 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA F 326 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE F 297 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 127 through 148 removed outlier: 6.727A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 173 current: chain 'F' and resid 200 through 207 removed outlier: 6.543A pdb=" N LEU F 224 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC7, first strand: chain 'G' and resid 1049 through 1052 removed outlier: 4.644A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE G1024 " --> pdb=" O MET G1082 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR G1084 " --> pdb=" O PHE G1024 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL G1026 " --> pdb=" O THR G1084 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU G1134 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU G1106 " --> pdb=" O LEU G1134 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE G 994 " --> pdb=" O LEU G1199 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1214 through 1217 removed outlier: 6.600A pdb=" N ILE G1214 " --> pdb=" O VAL G1673 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ARG G1675 " --> pdb=" O ILE G1214 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE G1216 " --> pdb=" O ARG G1675 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL G1643 " --> pdb=" O TYR G1674 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU G1573 " --> pdb=" O ILE G1644 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL G1572 " --> pdb=" O PHE G1624 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU G1626 " --> pdb=" O VAL G1572 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU G1574 " --> pdb=" O LEU G1626 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS G1597 " --> pdb=" O LEU G1625 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N SER G1627 " --> pdb=" O CYS G1597 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU G1599 " --> pdb=" O SER G1627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.315A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 1286 through 1287 Processing sheet with id=AD2, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.385A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.632A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AD5, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.350A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 97 through 100 Processing sheet with id=AD7, first strand: chain 'J' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 222 through 223 current: chain 'J' and resid 718 through 720 Processing sheet with id=AD8, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.756A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AE1, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.038A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AE3, first strand: chain 'O' and resid 100 through 102 Processing sheet with id=AE4, first strand: chain 'Q' and resid 118 through 119 1675 hydrogen bonds defined for protein. 4824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 300 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 12.53 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12427 1.34 - 1.46: 6695 1.46 - 1.57: 22013 1.57 - 1.69: 460 1.69 - 1.81: 279 Bond restraints: 41874 Sorted by residual: bond pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C4' DG K 25 " pdb=" C3' DG K 25 " ideal model delta sigma weight residual 1.529 1.578 -0.049 1.00e-02 1.00e+04 2.43e+01 bond pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C3' DT L -24 " pdb=" C2' DT L -24 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.40e+01 bond pdb=" C4' DC K 4 " pdb=" C3' DC K 4 " ideal model delta sigma weight residual 1.529 1.577 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 41869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.21: 57549 14.21 - 28.41: 4 28.41 - 42.62: 0 42.62 - 56.83: 0 56.83 - 71.03: 2 Bond angle restraints: 57555 Sorted by residual: angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F2 ALF G2003 " ideal model delta sigma weight residual 108.68 179.71 -71.03 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 109.63 179.74 -70.11 3.00e+00 1.11e-01 5.46e+02 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 110.21 89.49 20.72 3.00e+00 1.11e-01 4.77e+01 angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.69 89.50 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.59 90.27 19.32 3.00e+00 1.11e-01 4.15e+01 ... (remaining 57550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 23653 35.30 - 70.59: 1184 70.59 - 105.89: 63 105.89 - 141.18: 5 141.18 - 176.48: 5 Dihedral angle restraints: 24910 sinusoidal: 11451 harmonic: 13459 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 123.52 176.48 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 126.85 173.14 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PB ADP G2001 " pdb=" PA ADP G2001 " ideal model delta sinusoidal sigma weight residual 300.00 139.58 160.41 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 24907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4869 0.061 - 0.122: 1499 0.122 - 0.182: 173 0.182 - 0.243: 14 0.243 - 0.304: 1 Chirality restraints: 6556 Sorted by residual: chirality pdb=" CB ILE O 79 " pdb=" CA ILE O 79 " pdb=" CG1 ILE O 79 " pdb=" CG2 ILE O 79 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU G1626 " pdb=" CB LEU G1626 " pdb=" CD1 LEU G1626 " pdb=" CD2 LEU G1626 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE F 356 " pdb=" N ILE F 356 " pdb=" C ILE F 356 " pdb=" CB ILE F 356 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 6553 not shown) Planarity restraints: 6657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G1086 " 0.003 2.00e-02 2.50e+03 3.44e-02 2.36e+01 pdb=" CG TYR G1086 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR G1086 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR G1086 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR G1086 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR G1086 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G1086 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR G1086 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 437 " 0.382 9.50e-02 1.11e+02 1.72e-01 2.27e+01 pdb=" NE ARG F 437 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG F 437 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG F 437 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG F 437 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC L -25 " 0.053 2.00e-02 2.50e+03 3.11e-02 2.18e+01 pdb=" N1 DC L -25 " -0.075 2.00e-02 2.50e+03 pdb=" C2 DC L -25 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC L -25 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DC L -25 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC L -25 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC L -25 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DC L -25 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC L -25 " -0.002 2.00e-02 2.50e+03 ... (remaining 6654 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 12 2.40 - 3.03: 23265 3.03 - 3.65: 62178 3.65 - 4.28: 101088 4.28 - 4.90: 161010 Nonbonded interactions: 347553 Sorted by model distance: nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 1.775 2.170 nonbonded pdb="MG MG G2002 " pdb=" F3 ALF G2003 " model vdw 1.877 2.120 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 1.997 2.170 nonbonded pdb=" O2B ADP G2001 " pdb="MG MG G2002 " model vdw 2.018 2.170 nonbonded pdb=" N2 DG K -68 " pdb=" O2 DT L 69 " model vdw 2.193 3.120 ... (remaining 347548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'F' and resid 20 through 501) } ncs_group { reference = (chain 'N' and resid 23 through 93) selection = (chain 'R' and resid 23 through 93) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.680 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: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 43.360 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 0.471 41875 Z= 0.433 Angle : 1.065 71.033 57555 Z= 0.579 Chirality : 0.055 0.304 6556 Planarity : 0.011 0.172 6657 Dihedral : 18.214 176.478 16228 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.11), residues: 4623 helix: -1.31 (0.09), residues: 2169 sheet: 0.49 (0.20), residues: 617 loop : -0.14 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.004 ARG F 437 TYR 0.053 0.006 TYR G1086 PHE 0.049 0.003 PHE G1047 TRP 0.075 0.003 TRP G1650 HIS 0.012 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.37 (41874) covalent geometry : angle 1.06483 / 0.58 (57555) hydrogen bonds : bond 0.19805 / 13.30 ( 1825) hydrogen bonds : angle 7.73093 / 5.37 ( 5124) Misc. bond : bond 0.47059 / 24.77 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 810 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7787 (mtm) cc_final: 0.7556 (mmp) REVERT: B 133 GLU cc_start: 0.8112 (tt0) cc_final: 0.7835 (tp30) REVERT: B 250 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.6944 (tmt90) REVERT: B 421 ASN cc_start: 0.7254 (m-40) cc_final: 0.6978 (m-40) REVERT: C 394 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7804 (ttt-90) REVERT: C 458 HIS cc_start: 0.7634 (m-70) cc_final: 0.7389 (m-70) REVERT: E 217 MET cc_start: 0.8478 (mmm) cc_final: 0.8274 (mmm) REVERT: F 263 ASP cc_start: 0.7940 (t70) cc_final: 0.7691 (t0) REVERT: G 1099 MET cc_start: 0.7799 (tpt) cc_final: 0.7508 (tpt) REVERT: G 1145 GLU cc_start: 0.6855 (tt0) cc_final: 0.6604 (mm-30) REVERT: G 1258 MET cc_start: 0.4807 (mmm) cc_final: 0.2897 (tpt) REVERT: G 1262 MET cc_start: 0.6363 (tpp) cc_final: 0.6039 (tpt) REVERT: J 19 TRP cc_start: 0.8958 (p90) cc_final: 0.8446 (p90) REVERT: J 174 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7776 (mt-10) REVERT: M 106 ASP cc_start: 0.7492 (m-30) cc_final: 0.7208 (m-30) REVERT: M 129 ARG cc_start: 0.7585 (tpt-90) cc_final: 0.7148 (tpt90) REVERT: N 25 ASN cc_start: 0.6830 (m-40) cc_final: 0.6371 (m-40) REVERT: N 31 LYS cc_start: 0.7873 (mttt) cc_final: 0.7650 (mttp) REVERT: N 93 GLN cc_start: 0.6398 (mt0) cc_final: 0.6004 (mm-40) REVERT: O 38 ASN cc_start: 0.8247 (t0) cc_final: 0.8036 (t0) REVERT: O 74 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7544 (mmtt) REVERT: O 94 ASN cc_start: 0.7859 (t0) cc_final: 0.7604 (t0) REVERT: O 99 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.6888 (mtp85) REVERT: P 40 LYS cc_start: 0.7785 (mttt) cc_final: 0.7099 (mmtt) REVERT: P 54 LYS cc_start: 0.7396 (ttmt) cc_final: 0.7151 (mtmm) REVERT: P 59 MET cc_start: 0.8089 (mmm) cc_final: 0.7700 (mmm) REVERT: P 65 ASP cc_start: 0.8145 (t70) cc_final: 0.7721 (t0) REVERT: Q 68 GLN cc_start: 0.7529 (mt0) cc_final: 0.7317 (mt0) REVERT: R 53 GLU cc_start: 0.8304 (tp30) cc_final: 0.7903 (tp30) REVERT: R 77 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7963 (mttm) REVERT: R 95 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7126 (mtp85) outliers start: 0 outliers final: 1 residues processed: 810 average time/residue: 0.9352 time to fit residues: 885.3020 Evaluate side-chains 457 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 112 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 146 ASN A 168 GLN A 248 ASN A 421 ASN B 19 HIS B 263 GLN C 86 GLN C 230 HIS C 421 ASN D 24 HIS D 328 ASN D 359 HIS E 24 HIS E 225 GLN F 452 ASN G1034 HIS G1141 ASN G1345 HIS G1657 GLN ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN J 633 ASN J 654 GLN J 696 GLN P 44 GLN P 60 ASN P 81 ASN Q 125 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.109461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.089879 restraints weight = 69449.415| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.76 r_work: 0.3236 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 41875 Z= 0.175 Angle : 0.766 29.382 57555 Z= 0.394 Chirality : 0.048 0.243 6556 Planarity : 0.005 0.055 6657 Dihedral : 20.975 158.874 7540 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.12 % Allowed : 9.22 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4623 helix: 0.30 (0.10), residues: 2197 sheet: 0.54 (0.20), residues: 595 loop : 0.15 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 112 TYR 0.020 0.002 TYR A 193 PHE 0.028 0.002 PHE G1264 TRP 0.024 0.002 TRP G1650 HIS 0.008 0.001 HIS G1345 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (41874) covalent geometry : angle 0.76604 / 0.39 (57555) hydrogen bonds : bond 0.05523 / 3.74 ( 1825) hydrogen bonds : angle 5.01546 / 3.48 ( 5124) Misc. bond : bond 0.01395 / 0.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 511 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7935 (mtm) cc_final: 0.7602 (mmt) REVERT: A 419 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7705 (ttm170) REVERT: B 60 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7713 (m90) REVERT: B 133 GLU cc_start: 0.8303 (tt0) cc_final: 0.8008 (tp30) REVERT: B 250 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7268 (tmt90) REVERT: B 423 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7644 (mpp80) REVERT: D 200 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8508 (tppt) REVERT: D 222 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8142 (mtpp) REVERT: D 235 LYS cc_start: 0.8654 (tttt) cc_final: 0.8345 (ptmt) REVERT: D 285 GLU cc_start: 0.7660 (tt0) cc_final: 0.7225 (mt-10) REVERT: E 273 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: F 133 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5803 (tm-30) REVERT: F 183 LYS cc_start: 0.8892 (tmmt) cc_final: 0.8609 (tptp) REVERT: F 263 ASP cc_start: 0.7929 (t70) cc_final: 0.7679 (t0) REVERT: F 419 GLN cc_start: 0.8578 (mt0) cc_final: 0.8368 (mt0) REVERT: G 1021 TRP cc_start: 0.7521 (m-90) cc_final: 0.7271 (m-10) REVERT: G 1047 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6605 (t80) REVERT: G 1258 MET cc_start: 0.4318 (mmm) cc_final: 0.2414 (tpt) REVERT: G 1479 ASP cc_start: 0.7754 (p0) cc_final: 0.7544 (p0) REVERT: H 463 GLU cc_start: 0.7650 (pm20) cc_final: 0.7419 (pm20) REVERT: I 31 ASN cc_start: 0.9009 (t0) cc_final: 0.8188 (t0) REVERT: J 94 MET cc_start: 0.6834 (ttm) cc_final: 0.6522 (ttm) REVERT: J 717 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7607 (ttp-170) REVERT: M 129 ARG cc_start: 0.7863 (tpt-90) cc_final: 0.7512 (tpt90) REVERT: N 88 TYR cc_start: 0.7761 (m-80) cc_final: 0.7536 (m-80) REVERT: O 94 ASN cc_start: 0.7719 (t0) cc_final: 0.7518 (t0) REVERT: O 99 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7271 (mtp85) REVERT: P 40 LYS cc_start: 0.7874 (mttt) cc_final: 0.7333 (mmtt) REVERT: P 54 LYS cc_start: 0.7421 (ttmt) cc_final: 0.7214 (mtpm) REVERT: P 56 MET cc_start: 0.7595 (tpp) cc_final: 0.7319 (mmm) REVERT: P 83 ARG cc_start: 0.7695 (mmt-90) cc_final: 0.7461 (mtt90) REVERT: R 53 GLU cc_start: 0.8160 (tp30) cc_final: 0.7944 (tp30) REVERT: R 78 ARG cc_start: 0.6688 (ttp-110) cc_final: 0.6431 (mpp-170) REVERT: R 95 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7612 (mtp85) outliers start: 80 outliers final: 20 residues processed: 557 average time/residue: 0.9224 time to fit residues: 605.2777 Evaluate side-chains 448 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 421 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1047 PHE Chi-restraints excluded: chain G residue 1222 LEU Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1299 THR Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 347 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 461 optimal weight: 6.9990 chunk 299 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 263 GLN A 409 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN C 458 HIS D 359 HIS ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1141 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN J 63 ASN J 237 HIS J 259 ASN J 628 HIS J 633 ASN N 25 ASN P 81 ASN Q 68 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.107015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087386 restraints weight = 69539.455| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.77 r_work: 0.3191 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 41875 Z= 0.228 Angle : 0.762 30.653 57555 Z= 0.385 Chirality : 0.048 0.354 6556 Planarity : 0.006 0.076 6657 Dihedral : 21.143 153.655 7536 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.13 % Allowed : 11.82 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4623 helix: 0.42 (0.11), residues: 2223 sheet: 0.38 (0.20), residues: 613 loop : 0.01 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 234 TYR 0.027 0.002 TYR O 50 PHE 0.024 0.002 PHE G1079 TRP 0.021 0.002 TRP G1021 HIS 0.015 0.002 HIS J 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (41874) covalent geometry : angle 0.76238 / 0.39 (57555) hydrogen bonds : bond 0.05293 / 3.59 ( 1825) hydrogen bonds : angle 4.76827 / 3.31 ( 5124) Misc. bond : bond 0.01276 / 0.67 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 447 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9068 (tp) cc_final: 0.8756 (tp) REVERT: A 265 MET cc_start: 0.7962 (mtm) cc_final: 0.7576 (mmp) REVERT: A 286 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8169 (mttp) REVERT: A 419 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7649 (ttm170) REVERT: B 60 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7992 (m90) REVERT: B 250 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7371 (tmt90) REVERT: C 143 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: C 179 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: D 112 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: D 200 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8540 (tppt) REVERT: D 222 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8231 (mtpp) REVERT: D 235 LYS cc_start: 0.8709 (tttt) cc_final: 0.8448 (ptmt) REVERT: D 283 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8756 (tttm) REVERT: E 96 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7900 (tp40) REVERT: E 183 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8172 (ttpt) REVERT: E 273 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: F 133 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5737 (tm-30) REVERT: F 217 MET cc_start: 0.8310 (mmt) cc_final: 0.8023 (mmt) REVERT: F 263 ASP cc_start: 0.7963 (t70) cc_final: 0.7688 (t0) REVERT: F 364 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: F 419 GLN cc_start: 0.8664 (mt0) cc_final: 0.8432 (mt0) REVERT: F 446 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: G 1009 SER cc_start: 0.7835 (p) cc_final: 0.7577 (t) REVERT: G 1019 ASP cc_start: 0.7143 (m-30) cc_final: 0.6739 (t0) REVERT: G 1047 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6688 (t80) REVERT: G 1217 ASP cc_start: 0.7007 (t0) cc_final: 0.6724 (t0) REVERT: G 1262 MET cc_start: 0.5845 (tpp) cc_final: 0.5603 (tpt) REVERT: G 1479 ASP cc_start: 0.7871 (p0) cc_final: 0.7653 (p0) REVERT: G 1629 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6299 (mtm180) REVERT: H 463 GLU cc_start: 0.7711 (pm20) cc_final: 0.7471 (pm20) REVERT: H 464 GLU cc_start: 0.8138 (mp0) cc_final: 0.7719 (mp0) REVERT: I 14 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8607 (tp-100) REVERT: I 18 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7956 (mm-30) REVERT: J 34 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7604 (ptp90) REVERT: M 129 ARG cc_start: 0.7996 (tpt-90) cc_final: 0.7608 (tpt90) REVERT: N 39 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7329 (ttp-110) REVERT: N 92 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7573 (mtp-110) REVERT: O 99 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7299 (mtp85) REVERT: O 104 GLN cc_start: 0.8155 (mt0) cc_final: 0.7954 (mt0) REVERT: P 56 MET cc_start: 0.7613 (tpp) cc_final: 0.7334 (mmm) REVERT: Q 92 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6852 (mt) REVERT: R 78 ARG cc_start: 0.6672 (ttp-110) cc_final: 0.6456 (mtt180) REVERT: R 95 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7550 (mtp85) outliers start: 118 outliers final: 32 residues processed: 522 average time/residue: 0.9252 time to fit residues: 570.9933 Evaluate side-chains 449 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1047 PHE Chi-restraints excluded: chain G residue 1144 GLN Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 298 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 422 optimal weight: 20.0000 chunk 242 optimal weight: 0.9980 chunk 415 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 421 ASN C 60 HIS ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 HIS D 359 HIS F 96 GLN ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN J 633 ASN P 81 ASN Q 68 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087895 restraints weight = 69349.625| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.77 r_work: 0.3203 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 41875 Z= 0.182 Angle : 0.713 31.018 57555 Z= 0.354 Chirality : 0.046 0.321 6556 Planarity : 0.005 0.061 6657 Dihedral : 20.986 146.705 7536 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.44 % Allowed : 13.84 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.12), residues: 4623 helix: 0.68 (0.11), residues: 2223 sheet: 0.41 (0.20), residues: 639 loop : -0.03 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 234 TYR 0.022 0.002 TYR J 106 PHE 0.018 0.002 PHE G1079 TRP 0.019 0.002 TRP G1650 HIS 0.020 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (41874) covalent geometry : angle 0.71282 / 0.35 (57555) hydrogen bonds : bond 0.04515 / 3.08 ( 1825) hydrogen bonds : angle 4.58105 / 3.18 ( 5124) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 443 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9054 (tp) cc_final: 0.8732 (tp) REVERT: A 265 MET cc_start: 0.7949 (mtm) cc_final: 0.7562 (mmt) REVERT: A 286 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8129 (mttp) REVERT: A 334 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8493 (mmt180) REVERT: A 419 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7672 (ttm170) REVERT: B 60 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.8023 (m90) REVERT: B 133 GLU cc_start: 0.8273 (tt0) cc_final: 0.7988 (tp30) REVERT: B 250 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7339 (tmt90) REVERT: B 397 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: B 423 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7671 (mpp80) REVERT: C 44 CYS cc_start: 0.8598 (m) cc_final: 0.8292 (m) REVERT: C 130 ASP cc_start: 0.8660 (t0) cc_final: 0.8443 (t0) REVERT: C 143 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8086 (mm-30) REVERT: D 112 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: D 200 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8540 (tppt) REVERT: D 235 LYS cc_start: 0.8713 (tttt) cc_final: 0.8482 (ptmt) REVERT: D 283 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8796 (tttm) REVERT: E 67 LYS cc_start: 0.8301 (mtmp) cc_final: 0.7817 (mmtt) REVERT: E 112 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: E 183 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8165 (ttpt) REVERT: E 273 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: F 133 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5772 (tm-30) REVERT: F 183 LYS cc_start: 0.8766 (tmmt) cc_final: 0.8565 (tptp) REVERT: F 263 ASP cc_start: 0.7947 (t70) cc_final: 0.7723 (t0) REVERT: F 364 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: F 384 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8004 (t70) REVERT: F 419 GLN cc_start: 0.8676 (mt0) cc_final: 0.8448 (mt0) REVERT: F 446 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: G 1009 SER cc_start: 0.7900 (p) cc_final: 0.7642 (t) REVERT: G 1019 ASP cc_start: 0.7228 (m-30) cc_final: 0.6738 (t0) REVERT: G 1021 TRP cc_start: 0.7791 (m100) cc_final: 0.7245 (m100) REVERT: G 1104 MET cc_start: 0.7322 (ttm) cc_final: 0.6900 (ttt) REVERT: G 1217 ASP cc_start: 0.6927 (t0) cc_final: 0.6636 (t0) REVERT: G 1258 MET cc_start: 0.3971 (mtt) cc_final: 0.1955 (tpt) REVERT: G 1262 MET cc_start: 0.5919 (tpp) cc_final: 0.5671 (tpt) REVERT: G 1404 GLN cc_start: 0.8740 (tt0) cc_final: 0.8460 (tt0) REVERT: G 1629 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6430 (mtm180) REVERT: H 463 GLU cc_start: 0.7688 (pm20) cc_final: 0.7436 (pm20) REVERT: H 464 GLU cc_start: 0.8172 (mp0) cc_final: 0.7728 (mp0) REVERT: J 90 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7914 (tpt-90) REVERT: M 129 ARG cc_start: 0.7958 (tpt-90) cc_final: 0.7583 (tpt90) REVERT: N 39 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7344 (ttp-110) REVERT: N 92 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7583 (mtp-110) REVERT: O 99 ARG cc_start: 0.7871 (mmt-90) cc_final: 0.7297 (mtp85) REVERT: P 56 MET cc_start: 0.7501 (tpp) cc_final: 0.7242 (mmm) REVERT: R 78 ARG cc_start: 0.6665 (ttp-110) cc_final: 0.6377 (mtt180) REVERT: R 95 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7552 (mtp85) outliers start: 92 outliers final: 35 residues processed: 507 average time/residue: 0.8844 time to fit residues: 533.8484 Evaluate side-chains 455 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 402 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1085 SER Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1362 ILE Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 349 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 400 optimal weight: 5.9990 chunk 461 optimal weight: 0.0570 chunk 56 optimal weight: 3.9990 chunk 267 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN C 60 HIS C 458 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS E 65 GLN E 359 HIS F 96 GLN ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 ASN J 259 ASN O 38 ASN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.088246 restraints weight = 69206.084| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.77 r_work: 0.3210 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41875 Z= 0.161 Angle : 0.686 31.064 57555 Z= 0.339 Chirality : 0.045 0.315 6556 Planarity : 0.005 0.057 6657 Dihedral : 20.843 139.637 7536 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.52 % Allowed : 14.61 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 4623 helix: 0.83 (0.11), residues: 2229 sheet: 0.41 (0.20), residues: 642 loop : -0.05 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 34 TYR 0.019 0.002 TYR P 80 PHE 0.022 0.002 PHE G1264 TRP 0.018 0.002 TRP G1415 HIS 0.007 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (41874) covalent geometry : angle 0.68626 / 0.34 (57555) hydrogen bonds : bond 0.04218 / 2.88 ( 1825) hydrogen bonds : angle 4.44876 / 3.08 ( 5124) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 441 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9053 (tp) cc_final: 0.8725 (tp) REVERT: A 265 MET cc_start: 0.7969 (mtm) cc_final: 0.7563 (mmt) REVERT: A 286 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8133 (mttp) REVERT: A 334 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8486 (mmt180) REVERT: B 60 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7991 (m90) REVERT: B 133 GLU cc_start: 0.8288 (tt0) cc_final: 0.7995 (tp30) REVERT: B 250 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7301 (tmt90) REVERT: B 397 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: B 423 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7590 (mpp80) REVERT: B 442 ARG cc_start: 0.7448 (mtm110) cc_final: 0.7144 (mtm-85) REVERT: C 44 CYS cc_start: 0.8609 (m) cc_final: 0.8303 (m) REVERT: C 130 ASP cc_start: 0.8631 (t0) cc_final: 0.8415 (t0) REVERT: C 245 ASP cc_start: 0.8447 (m-30) cc_final: 0.8150 (m-30) REVERT: C 260 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: D 200 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8422 (mmpt) REVERT: D 235 LYS cc_start: 0.8710 (tttt) cc_final: 0.8489 (ptmt) REVERT: D 283 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8800 (tttm) REVERT: E 183 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8168 (ttpt) REVERT: E 273 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: F 133 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.5768 (tm-30) REVERT: F 183 LYS cc_start: 0.8784 (tmmt) cc_final: 0.8562 (tptp) REVERT: F 217 MET cc_start: 0.8245 (mmt) cc_final: 0.7974 (mmt) REVERT: F 263 ASP cc_start: 0.7906 (t70) cc_final: 0.7661 (t0) REVERT: F 299 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: F 364 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: F 384 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8008 (t70) REVERT: F 419 GLN cc_start: 0.8666 (mt0) cc_final: 0.8440 (mt0) REVERT: F 446 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8070 (tp30) REVERT: G 1009 SER cc_start: 0.7973 (p) cc_final: 0.7685 (t) REVERT: G 1217 ASP cc_start: 0.7011 (t0) cc_final: 0.6758 (t0) REVERT: G 1262 MET cc_start: 0.6006 (tpp) cc_final: 0.5757 (tpt) REVERT: G 1665 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7302 (mt) REVERT: I 14 GLN cc_start: 0.8975 (tm-30) cc_final: 0.7165 (tp-100) REVERT: J 90 ARG cc_start: 0.8177 (tpt-90) cc_final: 0.7941 (tpt-90) REVERT: J 94 MET cc_start: 0.7159 (ttm) cc_final: 0.6821 (ttm) REVERT: M 129 ARG cc_start: 0.7976 (tpt-90) cc_final: 0.7568 (tpt90) REVERT: N 91 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7599 (mptt) REVERT: N 92 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7624 (mtp-110) REVERT: O 99 ARG cc_start: 0.7868 (mmt-90) cc_final: 0.7279 (mtp85) REVERT: P 54 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7143 (mtmm) REVERT: R 78 ARG cc_start: 0.6739 (ttp-110) cc_final: 0.6524 (mtt180) REVERT: R 95 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7520 (mtp85) outliers start: 95 outliers final: 32 residues processed: 508 average time/residue: 0.9037 time to fit residues: 546.5321 Evaluate side-chains 451 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 402 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1047 PHE Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 92 optimal weight: 3.9990 chunk 470 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 423 optimal weight: 20.0000 chunk 451 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 465 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN C 60 HIS C 458 HIS D 359 HIS D 375 GLN E 254 GLN O 38 ASN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.109062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089894 restraints weight = 69455.914| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.97 r_work: 0.3228 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41875 Z= 0.123 Angle : 0.658 30.341 57555 Z= 0.324 Chirality : 0.043 0.308 6556 Planarity : 0.004 0.071 6657 Dihedral : 20.654 133.726 7536 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.78 % Allowed : 15.99 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4623 helix: 1.07 (0.11), residues: 2221 sheet: 0.51 (0.20), residues: 638 loop : 0.04 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 234 TYR 0.016 0.001 TYR A 193 PHE 0.027 0.001 PHE G1264 TRP 0.017 0.001 TRP G1415 HIS 0.009 0.001 HIS G1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (41874) covalent geometry : angle 0.65758 / 0.32 (57555) hydrogen bonds : bond 0.03755 / 2.56 ( 1825) hydrogen bonds : angle 4.29698 / 2.97 ( 5124) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 438 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9044 (tp) cc_final: 0.8728 (tp) REVERT: A 265 MET cc_start: 0.7949 (mtm) cc_final: 0.7531 (mmt) REVERT: B 133 GLU cc_start: 0.8311 (tt0) cc_final: 0.8074 (tp30) REVERT: B 179 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 269 MET cc_start: 0.7952 (mtm) cc_final: 0.6979 (mmt) REVERT: B 423 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7692 (mpp80) REVERT: B 442 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7178 (mtm-85) REVERT: C 44 CYS cc_start: 0.8646 (m) cc_final: 0.8334 (m) REVERT: C 130 ASP cc_start: 0.8574 (t0) cc_final: 0.8335 (t0) REVERT: C 245 ASP cc_start: 0.8429 (m-30) cc_final: 0.8146 (m-30) REVERT: C 304 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8376 (mm-30) REVERT: D 200 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8417 (mmpt) REVERT: D 235 LYS cc_start: 0.8685 (tttt) cc_final: 0.8109 (ptmt) REVERT: E 183 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8173 (ttpt) REVERT: E 212 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8069 (ttp-110) REVERT: E 273 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: F 109 PHE cc_start: 0.8878 (m-80) cc_final: 0.8620 (m-80) REVERT: F 133 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.5866 (tm-30) REVERT: F 183 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8534 (tptp) REVERT: F 217 MET cc_start: 0.8217 (mmt) cc_final: 0.7955 (mmt) REVERT: F 263 ASP cc_start: 0.7851 (t70) cc_final: 0.7635 (t0) REVERT: F 299 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: F 384 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8034 (t70) REVERT: F 419 GLN cc_start: 0.8664 (mt0) cc_final: 0.8436 (mt0) REVERT: G 1009 SER cc_start: 0.8026 (p) cc_final: 0.7711 (t) REVERT: G 1217 ASP cc_start: 0.7025 (t0) cc_final: 0.6771 (t0) REVERT: G 1262 MET cc_start: 0.5994 (tpp) cc_final: 0.5773 (tpt) REVERT: G 1327 ASP cc_start: 0.7776 (p0) cc_final: 0.7546 (p0) REVERT: G 1629 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6381 (mtm180) REVERT: G 1665 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7223 (mt) REVERT: J 90 ARG cc_start: 0.8194 (tpt-90) cc_final: 0.7955 (tpt-90) REVERT: M 129 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7544 (tpt90) REVERT: N 91 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7567 (mptt) REVERT: O 99 ARG cc_start: 0.7840 (mmt-90) cc_final: 0.7268 (mtp85) REVERT: P 54 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7118 (mtmm) REVERT: R 78 ARG cc_start: 0.6785 (ttp-110) cc_final: 0.6537 (mtt180) REVERT: R 95 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7518 (mtp85) outliers start: 67 outliers final: 23 residues processed: 486 average time/residue: 0.9010 time to fit residues: 521.9912 Evaluate side-chains 437 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 402 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 392 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 349 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN B 421 ASN C 60 HIS C 458 HIS D 359 HIS D 375 GLN E 24 HIS ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN F 301 HIS ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS G1259 ASN G1263 GLN J 114 HIS J 298 GLN O 38 ASN P 60 ASN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087391 restraints weight = 69793.219| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.96 r_work: 0.3181 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 41875 Z= 0.211 Angle : 0.718 31.963 57555 Z= 0.355 Chirality : 0.046 0.317 6556 Planarity : 0.005 0.081 6657 Dihedral : 20.790 133.721 7536 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.31 % Allowed : 16.47 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 4623 helix: 0.89 (0.11), residues: 2230 sheet: 0.43 (0.20), residues: 640 loop : -0.07 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 112 TYR 0.027 0.002 TYR P 80 PHE 0.026 0.002 PHE G1264 TRP 0.022 0.002 TRP G1036 HIS 0.008 0.001 HIS J 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (41874) covalent geometry : angle 0.71760 / 0.35 (57555) hydrogen bonds : bond 0.04397 / 3.00 ( 1825) hydrogen bonds : angle 4.42949 / 3.06 ( 5124) Misc. bond : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 414 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9052 (tp) cc_final: 0.8723 (tp) REVERT: A 265 MET cc_start: 0.7961 (mtm) cc_final: 0.7498 (mmt) REVERT: A 334 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8563 (mmt180) REVERT: B 133 GLU cc_start: 0.8321 (tt0) cc_final: 0.8003 (tp30) REVERT: B 423 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7674 (mpp80) REVERT: C 44 CYS cc_start: 0.8635 (m) cc_final: 0.8317 (m) REVERT: C 130 ASP cc_start: 0.8673 (t0) cc_final: 0.8452 (t0) REVERT: C 304 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: D 200 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8436 (mmpt) REVERT: D 283 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8822 (tttm) REVERT: E 112 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: E 183 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8168 (ttpt) REVERT: E 212 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8088 (ttp-110) REVERT: E 273 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: F 133 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.5902 (tm-30) REVERT: F 183 LYS cc_start: 0.8755 (tmmt) cc_final: 0.8508 (tptp) REVERT: F 217 MET cc_start: 0.8251 (mmt) cc_final: 0.7974 (mmt) REVERT: F 263 ASP cc_start: 0.7930 (t70) cc_final: 0.7700 (t0) REVERT: F 299 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: F 364 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: F 384 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8066 (t70) REVERT: G 1009 SER cc_start: 0.8075 (p) cc_final: 0.7793 (t) REVERT: G 1143 MET cc_start: 0.6929 (tpp) cc_final: 0.6501 (mmt) REVERT: G 1262 MET cc_start: 0.6018 (tpp) cc_final: 0.5788 (tpt) REVERT: G 1327 ASP cc_start: 0.7735 (p0) cc_final: 0.7484 (p0) REVERT: G 1629 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6451 (mtm180) REVERT: G 1665 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7269 (mt) REVERT: I 14 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8172 (tp-100) REVERT: I 30 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8351 (mtp-110) REVERT: I 210 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: J 34 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7553 (ptp90) REVERT: J 90 ARG cc_start: 0.8187 (tpt-90) cc_final: 0.7784 (ttm-80) REVERT: J 154 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7875 (mmm) REVERT: M 129 ARG cc_start: 0.7963 (tpt-90) cc_final: 0.7550 (tpt90) REVERT: N 39 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7311 (ttp-110) REVERT: N 91 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7616 (mptt) REVERT: O 99 ARG cc_start: 0.7887 (mmt-90) cc_final: 0.7285 (mtp85) REVERT: P 54 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7155 (mtmm) REVERT: R 78 ARG cc_start: 0.6791 (ttp-110) cc_final: 0.6512 (mtt180) REVERT: R 95 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7524 (mtp85) outliers start: 87 outliers final: 39 residues processed: 473 average time/residue: 0.8841 time to fit residues: 500.3903 Evaluate side-chains 448 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 390 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 986 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1047 PHE Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain R residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 177 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 424 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN C 60 HIS C 458 HIS D 359 HIS ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS G1259 ASN G1263 GLN G1300 ASN O 38 ASN P 60 ASN P 92 GLN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087029 restraints weight = 69738.397| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.94 r_work: 0.3175 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 41875 Z= 0.210 Angle : 0.721 32.140 57555 Z= 0.357 Chirality : 0.046 0.306 6556 Planarity : 0.005 0.087 6657 Dihedral : 20.839 133.703 7536 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 17.18 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.12), residues: 4623 helix: 0.83 (0.11), residues: 2230 sheet: 0.42 (0.20), residues: 633 loop : -0.15 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 21 TYR 0.021 0.002 TYR N 88 PHE 0.028 0.002 PHE G1264 TRP 0.025 0.002 TRP G1036 HIS 0.010 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (41874) covalent geometry : angle 0.72080 / 0.36 (57555) hydrogen bonds : bond 0.04408 / 3.02 ( 1825) hydrogen bonds : angle 4.45645 / 3.08 ( 5124) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 409 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9065 (tp) cc_final: 0.8747 (tp) REVERT: A 265 MET cc_start: 0.7990 (mtm) cc_final: 0.7574 (mmt) REVERT: A 334 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8524 (mmt180) REVERT: B 133 GLU cc_start: 0.8311 (tt0) cc_final: 0.8024 (tp30) REVERT: B 250 ARG cc_start: 0.8209 (ptm160) cc_final: 0.7588 (ptp-110) REVERT: B 423 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7725 (mpp80) REVERT: C 44 CYS cc_start: 0.8604 (m) cc_final: 0.8301 (m) REVERT: C 130 ASP cc_start: 0.8655 (t0) cc_final: 0.8440 (t0) REVERT: C 304 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: D 200 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8458 (mmpt) REVERT: D 283 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8823 (tttm) REVERT: E 96 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7829 (tm-30) REVERT: E 112 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: E 183 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8222 (ttpt) REVERT: E 212 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8101 (ttp-110) REVERT: E 273 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: F 18 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7747 (mm) REVERT: F 133 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.5967 (tm-30) REVERT: F 183 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8530 (tptp) REVERT: F 217 MET cc_start: 0.8265 (mmt) cc_final: 0.7988 (mmt) REVERT: F 299 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: F 364 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: F 384 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8081 (t70) REVERT: G 1009 SER cc_start: 0.8049 (p) cc_final: 0.7786 (t) REVERT: G 1083 ILE cc_start: 0.7871 (mm) cc_final: 0.7596 (mp) REVERT: G 1143 MET cc_start: 0.6902 (tpp) cc_final: 0.6450 (mmt) REVERT: G 1262 MET cc_start: 0.5968 (tpp) cc_final: 0.5741 (tpt) REVERT: G 1629 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6466 (mtm180) REVERT: G 1665 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7227 (mt) REVERT: H 446 MET cc_start: 0.8604 (mmm) cc_final: 0.8263 (mtt) REVERT: I 14 GLN cc_start: 0.9023 (tm-30) cc_final: 0.7653 (tp-100) REVERT: J 34 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7598 (ptp90) REVERT: J 90 ARG cc_start: 0.8323 (tpt-90) cc_final: 0.8066 (tpt-90) REVERT: J 154 MET cc_start: 0.8210 (tpp) cc_final: 0.7992 (mmm) REVERT: M 129 ARG cc_start: 0.7979 (tpt-90) cc_final: 0.7596 (tpt90) REVERT: N 31 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7538 (ttpt) REVERT: N 39 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7282 (ttp-110) REVERT: O 99 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7356 (mtp85) REVERT: P 54 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7163 (mtmm) REVERT: R 78 ARG cc_start: 0.6815 (ttp-110) cc_final: 0.6555 (mtt180) REVERT: R 95 ARG cc_start: 0.8038 (mtt90) cc_final: 0.7561 (mtp85) outliers start: 81 outliers final: 43 residues processed: 465 average time/residue: 0.8994 time to fit residues: 499.8596 Evaluate side-chains 450 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 389 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1047 PHE Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1263 GLN Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 184 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 chunk 385 optimal weight: 8.9990 chunk 403 optimal weight: 0.8980 chunk 431 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 HIS C 458 HIS D 359 HIS ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1080 HIS G1263 GLN O 38 ASN P 60 ASN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.088731 restraints weight = 69760.387| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.75 r_work: 0.3219 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41875 Z= 0.140 Angle : 0.679 31.069 57555 Z= 0.336 Chirality : 0.044 0.307 6556 Planarity : 0.004 0.084 6657 Dihedral : 20.678 131.285 7536 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.67 % Allowed : 17.88 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4623 helix: 1.07 (0.11), residues: 2224 sheet: 0.49 (0.20), residues: 633 loop : -0.09 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 116 TYR 0.029 0.001 TYR N 88 PHE 0.015 0.001 PHE P 67 TRP 0.018 0.001 TRP G1036 HIS 0.010 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (41874) covalent geometry : angle 0.67885 / 0.34 (57555) hydrogen bonds : bond 0.03844 / 2.65 ( 1825) hydrogen bonds : angle 4.30801 / 2.98 ( 5124) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 411 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9052 (tp) cc_final: 0.8727 (tp) REVERT: A 265 MET cc_start: 0.7885 (mtm) cc_final: 0.7500 (mmt) REVERT: B 133 GLU cc_start: 0.8256 (tt0) cc_final: 0.7986 (tp30) REVERT: B 250 ARG cc_start: 0.8184 (ptm160) cc_final: 0.7563 (ptp-110) REVERT: B 423 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7741 (mpp80) REVERT: C 44 CYS cc_start: 0.8573 (m) cc_final: 0.8258 (m) REVERT: C 130 ASP cc_start: 0.8600 (t0) cc_final: 0.8366 (t0) REVERT: C 245 ASP cc_start: 0.8408 (m-30) cc_final: 0.8136 (m-30) REVERT: C 260 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8213 (mtp) REVERT: C 304 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: D 134 GLU cc_start: 0.7958 (tp30) cc_final: 0.7699 (tp30) REVERT: D 200 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8416 (mmpt) REVERT: E 96 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7785 (tm-30) REVERT: E 112 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: E 183 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8187 (ttpt) REVERT: E 212 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8070 (ttp-110) REVERT: E 273 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: F 109 PHE cc_start: 0.8814 (m-80) cc_final: 0.8562 (m-80) REVERT: F 133 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6025 (tm-30) REVERT: F 183 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8524 (tptp) REVERT: F 217 MET cc_start: 0.8220 (mmt) cc_final: 0.7947 (mmt) REVERT: F 299 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: F 384 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8086 (t70) REVERT: G 1009 SER cc_start: 0.8072 (p) cc_final: 0.7793 (t) REVERT: G 1083 ILE cc_start: 0.7814 (mm) cc_final: 0.7535 (mp) REVERT: G 1262 MET cc_start: 0.6207 (tpp) cc_final: 0.5997 (tpt) REVERT: G 1629 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6471 (mtm180) REVERT: G 1665 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7236 (mt) REVERT: H 446 MET cc_start: 0.8525 (mmm) cc_final: 0.8242 (mtt) REVERT: I 30 ARG cc_start: 0.8726 (mtp-110) cc_final: 0.8344 (mtp180) REVERT: J 34 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7602 (ptp90) REVERT: M 129 ARG cc_start: 0.7957 (tpt-90) cc_final: 0.7546 (tpt90) REVERT: N 31 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7503 (ttpt) REVERT: O 99 ARG cc_start: 0.7870 (mmt-90) cc_final: 0.7310 (mtp85) REVERT: P 54 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7195 (mtpm) REVERT: R 78 ARG cc_start: 0.6807 (ttp-110) cc_final: 0.6529 (mtt180) REVERT: R 95 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7508 (mtp85) outliers start: 63 outliers final: 36 residues processed: 455 average time/residue: 0.8803 time to fit residues: 477.3462 Evaluate side-chains 441 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 391 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1047 PHE Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1263 GLN Chi-restraints excluded: chain G residue 1346 MET Chi-restraints excluded: chain G residue 1620 GLU Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 413 optimal weight: 20.0000 chunk 446 optimal weight: 4.9990 chunk 381 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 420 optimal weight: 10.0000 chunk 432 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 243 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN C 60 HIS C 237 GLN C 458 HIS D 359 HIS ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS G1263 GLN G1593 ASN O 38 ASN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087521 restraints weight = 69402.089| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.77 r_work: 0.3197 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41875 Z= 0.188 Angle : 0.710 31.911 57555 Z= 0.352 Chirality : 0.045 0.317 6556 Planarity : 0.005 0.078 6657 Dihedral : 20.725 131.762 7536 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.70 % Allowed : 18.19 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 4623 helix: 0.99 (0.11), residues: 2225 sheet: 0.45 (0.20), residues: 655 loop : -0.12 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 21 TYR 0.037 0.002 TYR N 88 PHE 0.017 0.002 PHE G1079 TRP 0.025 0.002 TRP G1036 HIS 0.008 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (41874) covalent geometry : angle 0.71044 / 0.35 (57555) hydrogen bonds : bond 0.04203 / 2.89 ( 1825) hydrogen bonds : angle 4.37447 / 3.02 ( 5124) Misc. bond : bond 0.00030 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 399 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9053 (tp) cc_final: 0.8726 (tp) REVERT: A 265 MET cc_start: 0.7909 (mtm) cc_final: 0.7490 (mmt) REVERT: B 133 GLU cc_start: 0.8293 (tt0) cc_final: 0.7996 (tp30) REVERT: B 250 ARG cc_start: 0.8193 (ptm160) cc_final: 0.7526 (ptp-110) REVERT: B 423 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7749 (mpp80) REVERT: C 44 CYS cc_start: 0.8560 (m) cc_final: 0.8240 (m) REVERT: C 130 ASP cc_start: 0.8638 (t0) cc_final: 0.8399 (t0) REVERT: C 245 ASP cc_start: 0.8393 (m-30) cc_final: 0.8107 (m-30) REVERT: C 304 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8363 (mm-30) REVERT: D 134 GLU cc_start: 0.7959 (tp30) cc_final: 0.7655 (tp30) REVERT: D 200 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8403 (mmpt) REVERT: E 96 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7814 (tm-30) REVERT: E 112 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: E 183 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8201 (ttpt) REVERT: E 273 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: F 133 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6023 (tm-30) REVERT: F 183 LYS cc_start: 0.8774 (tmmt) cc_final: 0.8538 (tptp) REVERT: F 217 MET cc_start: 0.8214 (mmt) cc_final: 0.7948 (mmt) REVERT: F 263 ASP cc_start: 0.7897 (t70) cc_final: 0.7471 (t0) REVERT: F 299 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: F 364 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: F 384 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8115 (t70) REVERT: G 1009 SER cc_start: 0.8122 (p) cc_final: 0.7831 (t) REVERT: G 1083 ILE cc_start: 0.7855 (mm) cc_final: 0.7585 (mp) REVERT: G 1143 MET cc_start: 0.6911 (tpp) cc_final: 0.6381 (mmt) REVERT: G 1545 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7531 (ttt) REVERT: G 1629 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6438 (mtm180) REVERT: G 1665 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7216 (mt) REVERT: H 446 MET cc_start: 0.8492 (mmm) cc_final: 0.8255 (mtt) REVERT: I 30 ARG cc_start: 0.8774 (mtp-110) cc_final: 0.8454 (mtp180) REVERT: J 34 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7618 (ptp90) REVERT: J 154 MET cc_start: 0.7824 (mmm) cc_final: 0.7607 (mtm) REVERT: J 174 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8056 (mt-10) REVERT: M 129 ARG cc_start: 0.7940 (tpt-90) cc_final: 0.7529 (tpt90) REVERT: N 31 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7504 (ttpt) REVERT: O 99 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.7301 (mtp85) REVERT: P 54 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7145 (mtmm) REVERT: R 78 ARG cc_start: 0.6808 (ttp-110) cc_final: 0.6526 (mtt180) REVERT: R 95 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7534 (mtp85) outliers start: 64 outliers final: 35 residues processed: 444 average time/residue: 0.8364 time to fit residues: 442.9724 Evaluate side-chains 439 residues out of total 3927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 390 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1620 GLU Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1629 ARG Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 473 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 377 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 328 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 HIS C 458 HIS D 359 HIS ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS G1259 ASN G1263 GLN O 38 ASN Q 68 GLN Q 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.108825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089602 restraints weight = 69850.054| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.75 r_work: 0.3235 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41875 Z= 0.126 Angle : 0.669 30.884 57555 Z= 0.330 Chirality : 0.043 0.322 6556 Planarity : 0.004 0.050 6657 Dihedral : 20.557 129.161 7536 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.43 % Allowed : 18.65 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 4623 helix: 1.21 (0.11), residues: 2224 sheet: 0.49 (0.20), residues: 657 loop : -0.05 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 116 TYR 0.035 0.001 TYR N 88 PHE 0.018 0.001 PHE G1264 TRP 0.017 0.001 TRP G1650 HIS 0.008 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (41874) covalent geometry : angle 0.66905 / 0.33 (57555) hydrogen bonds : bond 0.03646 / 2.51 ( 1825) hydrogen bonds : angle 4.23062 / 2.93 ( 5124) Misc. bond : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19138.28 seconds wall clock time: 325 minutes 20.83 seconds (19520.83 seconds total)