Starting phenix.real_space_refine on Thu Mar 21 00:46:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxi_14200/03_2024/7qxi_14200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxi_14200/03_2024/7qxi_14200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxi_14200/03_2024/7qxi_14200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxi_14200/03_2024/7qxi_14200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxi_14200/03_2024/7qxi_14200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qxi_14200/03_2024/7qxi_14200.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 103 5.16 5 C 17908 2.51 5 N 5122 2.21 5 O 5723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C GLU 940": "OE1" <-> "OE2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C GLU 1020": "OE1" <-> "OE2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C GLU 1026": "OE1" <-> "OE2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C ARG 1246": "NH1" <-> "NH2" Residue "C ARG 1269": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1372": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M GLU 174": "OE1" <-> "OE2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M ARG 196": "NH1" <-> "NH2" Residue "M ARG 217": "NH1" <-> "NH2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M GLU 268": "OE1" <-> "OE2" Residue "M ARG 279": "NH1" <-> "NH2" Residue "M ARG 383": "NH1" <-> "NH2" Residue "M ARG 394": "NH1" <-> "NH2" Residue "M GLU 398": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28928 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2316 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 10125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10125 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 293 Chain: "D" Number of atoms: 9632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 9632 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 53, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 966 Unresolved non-hydrogen dihedrals: 649 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 22, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 10, 'GLU:plan': 29, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 477 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "M" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3162 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "N" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 15.46, per 1000 atoms: 0.53 Number of scatterers: 28928 At special positions: 0 Unit cell: (171.6, 176, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 72 15.00 O 5723 8.00 N 5122 7.00 C 17908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.11 Conformation dependent library (CDL) restraints added in 5.0 seconds 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6842 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 38 sheets defined 37.8% alpha, 9.4% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 9.97 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.839A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.890A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.995A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.100A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.832A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.503A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.979A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.643A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 4.532A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.725A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.641A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.643A pdb=" N ASN C 214 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.005A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 4.039A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.577A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.873A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.801A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.563A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 458 removed outlier: 3.599A pdb=" N GLU C 458 " --> pdb=" O SER C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 459 through 481 removed outlier: 3.658A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 removed outlier: 3.622A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.846A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.716A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.730A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 4.201A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.880A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 979 removed outlier: 3.548A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.703A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.583A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 1000' Processing helix chain 'C' and resid 1005 through 1037 removed outlier: 3.854A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.023A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.846A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1167 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1271 through 1280 removed outlier: 3.511A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C1280 " --> pdb=" O TRP C1276 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.842A pdb=" N THR C1292 " --> pdb=" O GLN C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.685A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 4.189A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 29 through 34 removed outlier: 3.703A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.788A pdb=" N ARG D 101 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.558A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 removed outlier: 4.110A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 181 through 191 removed outlier: 4.342A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.968A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 265 through 284 removed outlier: 3.982A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.567A pdb=" N LEU D 307 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 removed outlier: 3.861A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 332 " --> pdb=" O ASP D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 332' Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.139A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 4.373A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 513 Processing helix chain 'D' and resid 531 through 537 removed outlier: 3.591A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.993A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.864A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.616A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.624A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.612A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.639A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 753 removed outlier: 3.690A pdb=" N GLY D 752 " --> pdb=" O LYS D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.939A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 875 removed outlier: 4.101A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 removed outlier: 4.321A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 1139 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.945A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1224 through 1243 removed outlier: 4.043A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 4.054A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1294 removed outlier: 4.319A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D1294 " --> pdb=" O ARG D1290 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1323 removed outlier: 4.043A pdb=" N ALA D1323 " --> pdb=" O ILE D1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1362 through 1372 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.778A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 33 removed outlier: 3.532A pdb=" N ARG E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 4.033A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.705A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 removed outlier: 3.766A pdb=" N GLN M 21 " --> pdb=" O PRO M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 121 through 131 removed outlier: 3.515A pdb=" N GLU M 129 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 146 removed outlier: 3.593A pdb=" N SER M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 164 removed outlier: 3.814A pdb=" N ILE M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 182 removed outlier: 3.608A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE M 182 " --> pdb=" O VAL M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 212 through 222 removed outlier: 3.834A pdb=" N ASP M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 229 removed outlier: 4.116A pdb=" N LEU M 227 " --> pdb=" O HIS M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 239 removed outlier: 3.570A pdb=" N VAL M 238 " --> pdb=" O THR M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.581A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 263 Processing helix chain 'M' and resid 302 through 307 removed outlier: 3.658A pdb=" N ALA M 305 " --> pdb=" O GLN M 302 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET M 306 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 342 removed outlier: 3.575A pdb=" N GLY M 316 " --> pdb=" O ASN M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 351 Processing helix chain 'M' and resid 366 through 374 Processing helix chain 'M' and resid 377 through 386 Processing helix chain 'M' and resid 398 through 403 Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 465 removed outlier: 3.939A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 469 through 474 removed outlier: 3.574A pdb=" N LYS M 474 " --> pdb=" O SER M 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 5.020A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 105 removed outlier: 7.963A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.181A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.686A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.334A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.192A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.011A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 114 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.011A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.458A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.051A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 634 through 637 Processing sheet with id=AB9, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.895A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 723 through 727 removed outlier: 3.567A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'C' and resid 798 through 803 removed outlier: 3.610A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 798 through 803 removed outlier: 3.610A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.627A pdb=" N HIS C 832 " --> pdb=" O VAL C1056 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS C 838 " --> pdb=" O VAL C1050 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.627A pdb=" N HIS C 832 " --> pdb=" O VAL C1056 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AC8, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1336 Processing sheet with id=AD1, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.919A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AD3, first strand: chain 'D' and resid 365 through 369 Processing sheet with id=AD4, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD5, first strand: chain 'D' and resid 553 through 556 Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.676A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.229A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 843 through 844 removed outlier: 4.428A pdb=" N THR D 862 " --> pdb=" O THR D 844 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1002 through 1003 removed outlier: 3.749A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1265 through 1266 Processing sheet with id=AE2, first strand: chain 'M' and resid 47 through 48 removed outlier: 3.752A pdb=" N GLU M 48 " --> pdb=" O LYS M 298 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 13.93 Time building geometry restraints manager: 12.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4910 1.29 - 1.43: 6911 1.43 - 1.57: 17304 1.57 - 1.71: 182 1.71 - 1.85: 180 Bond restraints: 29487 Sorted by residual: bond pdb=" CA PRO M 258 " pdb=" C PRO M 258 " ideal model delta sigma weight residual 1.522 1.407 0.115 1.18e-02 7.18e+03 9.43e+01 bond pdb=" C4' DG N -10 " pdb=" O4' DG N -10 " ideal model delta sigma weight residual 1.450 1.605 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" CA LEU M 203 " pdb=" C LEU M 203 " ideal model delta sigma weight residual 1.522 1.420 0.102 1.37e-02 5.33e+03 5.59e+01 bond pdb=" C GLU M 48 " pdb=" O GLU M 48 " ideal model delta sigma weight residual 1.234 1.148 0.086 1.28e-02 6.10e+03 4.55e+01 bond pdb=" CA ASN M 44 " pdb=" C ASN M 44 " ideal model delta sigma weight residual 1.523 1.427 0.096 1.55e-02 4.16e+03 3.85e+01 ... (remaining 29482 not shown) Histogram of bond angle deviations from ideal: 82.72 - 93.17: 1 93.17 - 103.63: 563 103.63 - 114.09: 17657 114.09 - 124.55: 21478 124.55 - 135.00: 625 Bond angle restraints: 40324 Sorted by residual: angle pdb=" O3' DG N -10 " pdb=" P DA N -9 " pdb=" O5' DA N -9 " ideal model delta sigma weight residual 104.00 82.72 21.28 1.50e+00 4.44e-01 2.01e+02 angle pdb=" C ASN M 44 " pdb=" CA ASN M 44 " pdb=" CB ASN M 44 " ideal model delta sigma weight residual 110.44 101.89 8.55 9.00e-01 1.23e+00 9.02e+01 angle pdb=" C THR C 896 " pdb=" N PRO C 897 " pdb=" CA PRO C 897 " ideal model delta sigma weight residual 119.84 130.82 -10.98 1.25e+00 6.40e-01 7.72e+01 angle pdb=" C5' DG N -10 " pdb=" C4' DG N -10 " pdb=" O4' DG N -10 " ideal model delta sigma weight residual 109.40 96.49 12.91 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N ARG M 24 " pdb=" CA ARG M 24 " pdb=" C ARG M 24 " ideal model delta sigma weight residual 114.16 103.25 10.91 1.48e+00 4.57e-01 5.44e+01 ... (remaining 40319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 17165 34.54 - 69.07: 654 69.07 - 103.61: 18 103.61 - 138.14: 0 138.14 - 172.68: 1 Dihedral angle restraints: 17838 sinusoidal: 7242 harmonic: 10596 Sorted by residual: dihedral pdb=" C CYS M 346 " pdb=" N CYS M 346 " pdb=" CA CYS M 346 " pdb=" CB CYS M 346 " ideal model delta harmonic sigma weight residual -122.60 -138.03 15.43 0 2.50e+00 1.60e-01 3.81e+01 dihedral pdb=" C PRO M 258 " pdb=" N PRO M 258 " pdb=" CA PRO M 258 " pdb=" CB PRO M 258 " ideal model delta harmonic sigma weight residual -120.70 -106.06 -14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" CA ASP D 462 " pdb=" C ASP D 462 " pdb=" N GLY D 463 " pdb=" CA GLY D 463 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 17835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4631 0.130 - 0.260: 104 0.260 - 0.390: 18 0.390 - 0.520: 5 0.520 - 0.649: 4 Chirality restraints: 4762 Sorted by residual: chirality pdb=" CA CYS M 346 " pdb=" N CYS M 346 " pdb=" C CYS M 346 " pdb=" CB CYS M 346 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C4' DC N -13 " pdb=" C5' DC N -13 " pdb=" O4' DC N -13 " pdb=" C3' DC N -13 " both_signs ideal model delta sigma weight residual False -2.53 -1.90 -0.63 2.00e-01 2.50e+01 9.88e+00 chirality pdb=" C4' DG N -10 " pdb=" C5' DG N -10 " pdb=" O4' DG N -10 " pdb=" C3' DG N -10 " both_signs ideal model delta sigma weight residual False -2.53 -3.12 0.60 2.00e-01 2.50e+01 8.88e+00 ... (remaining 4759 not shown) Planarity restraints: 5045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 285 " 0.107 2.00e-02 2.50e+03 5.73e-02 8.22e+01 pdb=" CG TRP M 285 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP M 285 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP M 285 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP M 285 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP M 285 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP M 285 " -0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 285 " 0.065 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 285 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP M 285 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 17 " -0.053 2.00e-02 2.50e+03 2.36e-02 1.53e+01 pdb=" N9 DA T 17 " 0.045 2.00e-02 2.50e+03 pdb=" C8 DA T 17 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA T 17 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA T 17 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA T 17 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA T 17 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA T 17 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DA T 17 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DA T 17 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA T 17 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 44 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASN M 44 " 0.068 2.00e-02 2.50e+03 pdb=" O ASN M 44 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO M 45 " -0.023 2.00e-02 2.50e+03 ... (remaining 5042 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 474 2.64 - 3.21: 26267 3.21 - 3.77: 43606 3.77 - 4.34: 56337 4.34 - 4.90: 91509 Nonbonded interactions: 218193 Sorted by model distance: nonbonded pdb=" O GLN M 39 " pdb=" NE2 GLN M 39 " model vdw 2.078 2.520 nonbonded pdb=" O ARG M 279 " pdb=" NH1 ARG M 279 " model vdw 2.094 2.520 nonbonded pdb=" N ASP M 197 " pdb=" OD1 ASP M 197 " model vdw 2.135 2.520 nonbonded pdb=" N ASP M 225 " pdb=" OD1 ASP M 225 " model vdw 2.174 2.520 nonbonded pdb=" N GLU C 987 " pdb=" OE1 GLU C 987 " model vdw 2.186 2.520 ... (remaining 218188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 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: 1.390 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: 5.270 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 83.260 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 0.155 29487 Z= 0.375 Angle : 0.955 21.284 40324 Z= 0.620 Chirality : 0.058 0.649 4762 Planarity : 0.004 0.088 5045 Dihedral : 15.020 172.679 10996 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.36 % Favored : 91.87 % Rotamer: Outliers : 11.21 % Allowed : 8.63 % Favored : 80.15 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.12), residues: 3655 helix: -1.56 (0.13), residues: 1241 sheet: -2.39 (0.26), residues: 323 loop : -3.40 (0.11), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.005 TRP M 285 HIS 0.007 0.000 HIS M 377 PHE 0.039 0.001 PHE M 318 TYR 0.008 0.001 TYR D 679 ARG 0.005 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 795 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7393 (tt) REVERT: A 127 GLN cc_start: 0.8725 (mp10) cc_final: 0.8440 (mp10) REVERT: A 262 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6930 (mm) REVERT: A 312 LEU cc_start: 0.6953 (mt) cc_final: 0.6627 (mt) REVERT: A 313 SER cc_start: 0.7984 (t) cc_final: 0.7732 (p) REVERT: B 96 ASP cc_start: 0.6933 (m-30) cc_final: 0.6665 (t70) REVERT: B 130 ILE cc_start: 0.8975 (mm) cc_final: 0.8743 (mp) REVERT: B 147 GLN cc_start: 0.8206 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 186 ASN cc_start: 0.7947 (t0) cc_final: 0.7727 (t0) REVERT: C 183 TRP cc_start: 0.8249 (m-10) cc_final: 0.7920 (m-10) REVERT: C 203 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7535 (mtmm) REVERT: C 218 GLU cc_start: 0.8796 (pt0) cc_final: 0.8424 (tm-30) REVERT: C 503 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7695 (mttp) REVERT: C 524 ILE cc_start: 0.8851 (tt) cc_final: 0.8513 (tt) REVERT: C 542 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5992 (ttm170) REVERT: C 589 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7683 (t) REVERT: C 835 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: C 838 CYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8980 (p) REVERT: C 840 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7691 (t) REVERT: C 868 SER cc_start: 0.7102 (OUTLIER) cc_final: 0.6843 (t) REVERT: C 903 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8975 (mtp85) REVERT: C 925 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8841 (p) REVERT: C 962 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: C 1021 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8907 (tp) REVERT: C 1024 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8918 (mm-30) REVERT: C 1029 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8601 (tp) REVERT: C 1038 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: C 1057 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8458 (tttt) REVERT: C 1058 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7811 (mtt-85) REVERT: C 1161 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8086 (tt) REVERT: D 76 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7906 (ptmt) REVERT: D 165 TYR cc_start: 0.8273 (t80) cc_final: 0.8043 (t80) REVERT: D 227 PHE cc_start: 0.8809 (t80) cc_final: 0.8157 (t80) REVERT: D 321 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8313 (tppt) REVERT: D 330 MET cc_start: 0.6597 (ptp) cc_final: 0.6252 (ptp) REVERT: D 453 VAL cc_start: 0.8877 (p) cc_final: 0.8659 (t) REVERT: D 518 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.8017 (m) REVERT: D 695 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8337 (tptm) REVERT: D 788 LEU cc_start: 0.7844 (tt) cc_final: 0.7511 (mp) REVERT: D 1040 MET cc_start: 0.3379 (mtp) cc_final: 0.2563 (mmm) REVERT: E 7 GLN cc_start: 0.7729 (tp40) cc_final: 0.7512 (tp40) REVERT: E 60 ASN cc_start: 0.7984 (p0) cc_final: 0.7595 (p0) REVERT: E 63 ILE cc_start: 0.9198 (mm) cc_final: 0.8960 (mt) REVERT: M 42 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: M 115 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: M 117 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7052 (t) REVERT: M 173 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8815 (pm20) REVERT: M 185 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: M 196 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (tmm-80) REVERT: M 203 LEU cc_start: 0.9007 (mt) cc_final: 0.8799 (mp) REVERT: M 223 HIS cc_start: 0.9364 (m-70) cc_final: 0.9128 (m90) REVERT: M 252 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8808 (tp) REVERT: M 265 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: M 276 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6968 (p) REVERT: M 280 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7008 (mmmt) REVERT: M 306 MET cc_start: 0.8485 (mtt) cc_final: 0.7282 (mtm) REVERT: M 365 MET cc_start: 0.8353 (ptm) cc_final: 0.7634 (ptp) REVERT: M 378 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7026 (pp20) REVERT: M 400 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.4836 (mmtt) REVERT: M 441 LYS cc_start: 0.9723 (mtpm) cc_final: 0.8307 (tmtt) REVERT: M 455 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6285 (ptm-80) REVERT: M 456 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7972 (mmm160) outliers start: 313 outliers final: 109 residues processed: 1051 average time/residue: 0.4574 time to fit residues: 719.1863 Evaluate side-chains 521 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 375 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 LYS Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1051 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1237 HIS Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 387 GLN Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 391 HIS Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 400 LYS Chi-restraints excluded: chain M residue 455 ARG Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 0.2980 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 150 optimal weight: 0.0020 chunk 291 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 337 optimal weight: 6.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 227 GLN B 37 HIS C 513 GLN C 618 GLN C 965 GLN C1017 GLN C1038 GLN C1256 GLN C1314 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS M 34 GLN M 39 GLN M 127 GLN M 229 ASN M 254 GLN M 322 ASN M 387 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29487 Z= 0.255 Angle : 0.727 26.205 40324 Z= 0.353 Chirality : 0.045 0.205 4762 Planarity : 0.005 0.069 5045 Dihedral : 15.569 172.705 5080 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.85 % Favored : 92.01 % Rotamer: Outliers : 7.24 % Allowed : 17.48 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.13), residues: 3655 helix: -0.24 (0.15), residues: 1261 sheet: -1.95 (0.27), residues: 322 loop : -3.03 (0.11), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 321 HIS 0.011 0.001 HIS B 132 PHE 0.019 0.002 PHE M 318 TYR 0.020 0.002 TYR B 68 ARG 0.009 0.001 ARG D 731 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 402 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 SER cc_start: 0.8156 (t) cc_final: 0.7815 (p) REVERT: B 43 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 145 LYS cc_start: 0.8702 (ptpt) cc_final: 0.8194 (ptmm) REVERT: B 147 GLN cc_start: 0.8122 (tt0) cc_final: 0.7663 (tm-30) REVERT: B 186 ASN cc_start: 0.8015 (t0) cc_final: 0.7717 (t0) REVERT: C 156 PHE cc_start: 0.8549 (m-10) cc_final: 0.8222 (m-10) REVERT: C 183 TRP cc_start: 0.8030 (m-10) cc_final: 0.7666 (m100) REVERT: C 203 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7514 (mtmm) REVERT: C 385 PHE cc_start: 0.8677 (t80) cc_final: 0.8360 (t80) REVERT: C 407 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8269 (ttm170) REVERT: C 503 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7725 (mttp) REVERT: C 545 PHE cc_start: 0.7112 (t80) cc_final: 0.6791 (t80) REVERT: C 589 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8096 (t) REVERT: C 628 HIS cc_start: 0.7633 (m90) cc_final: 0.7270 (m-70) REVERT: C 639 LYS cc_start: 0.8358 (mmtm) cc_final: 0.7960 (mmtm) REVERT: C 903 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8941 (ptp-170) REVERT: C 954 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8909 (tptp) REVERT: C 1021 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8755 (tp) REVERT: C 1024 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8967 (mm-30) REVERT: C 1032 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8753 (ttpt) REVERT: C 1038 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: C 1051 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (mtpp) REVERT: C 1053 TYR cc_start: 0.8675 (m-80) cc_final: 0.8412 (m-80) REVERT: C 1304 MET cc_start: 0.8658 (tpp) cc_final: 0.8333 (tpp) REVERT: D 69 GLU cc_start: 0.6682 (pt0) cc_final: 0.6418 (pt0) REVERT: D 227 PHE cc_start: 0.8913 (t80) cc_final: 0.8598 (t80) REVERT: D 321 LYS cc_start: 0.8749 (pmtt) cc_final: 0.8370 (tppt) REVERT: D 375 GLU cc_start: 0.6653 (tp30) cc_final: 0.6448 (tp30) REVERT: D 398 LYS cc_start: 0.8982 (tttt) cc_final: 0.8538 (ttpp) REVERT: D 695 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8370 (tptm) REVERT: D 697 MET cc_start: 0.7624 (tpp) cc_final: 0.7392 (tmm) REVERT: D 788 LEU cc_start: 0.8155 (tt) cc_final: 0.7886 (mm) REVERT: D 868 TRP cc_start: 0.8432 (m-90) cc_final: 0.8210 (m-90) REVERT: D 1040 MET cc_start: 0.3163 (mtp) cc_final: 0.2610 (mmm) REVERT: E 10 VAL cc_start: 0.7984 (t) cc_final: 0.7635 (t) REVERT: E 43 ASN cc_start: 0.7703 (t0) cc_final: 0.7473 (t0) REVERT: M 28 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6298 (pt) REVERT: M 117 THR cc_start: 0.7615 (p) cc_final: 0.7155 (t) REVERT: M 181 ARG cc_start: 0.8615 (tmt170) cc_final: 0.8194 (tpt90) REVERT: M 203 LEU cc_start: 0.8973 (mt) cc_final: 0.8650 (tp) REVERT: M 212 TRP cc_start: 0.8461 (m-90) cc_final: 0.8181 (m-90) REVERT: M 270 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: M 276 VAL cc_start: 0.6547 (OUTLIER) cc_final: 0.6185 (p) REVERT: M 280 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (mmmt) REVERT: M 295 PRO cc_start: 0.8175 (Cg_exo) cc_final: 0.7910 (Cg_endo) REVERT: M 297 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6295 (mm) REVERT: M 306 MET cc_start: 0.8168 (mtt) cc_final: 0.7889 (mpp) REVERT: M 378 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: M 441 LYS cc_start: 0.9140 (mtpm) cc_final: 0.7799 (tmtt) REVERT: M 456 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8354 (mmm160) outliers start: 202 outliers final: 98 residues processed: 571 average time/residue: 0.4495 time to fit residues: 402.8382 Evaluate side-chains 427 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 311 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1051 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1237 HIS Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1303 LYS Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 0.0470 chunk 104 optimal weight: 1.9990 chunk 281 optimal weight: 0.4980 chunk 230 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 10.0000 chunk 365 optimal weight: 50.0000 chunk 301 optimal weight: 0.6980 chunk 335 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 283 GLN B 132 HIS C 150 HIS C 214 ASN C 238 GLN C 618 GLN C 965 GLN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 430 HIS ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS D1238 GLN M 229 ASN M 322 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29487 Z= 0.170 Angle : 0.643 17.390 40324 Z= 0.307 Chirality : 0.043 0.395 4762 Planarity : 0.004 0.057 5045 Dihedral : 14.497 172.777 4880 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 5.37 % Allowed : 19.67 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.13), residues: 3655 helix: 0.30 (0.15), residues: 1267 sheet: -1.68 (0.27), residues: 330 loop : -2.85 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 321 HIS 0.017 0.001 HIS D 430 PHE 0.022 0.001 PHE D 141 TYR 0.014 0.001 TYR C 346 ARG 0.009 0.000 ARG C1211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 353 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8255 (mm) REVERT: B 145 LYS cc_start: 0.8692 (ptpt) cc_final: 0.8209 (ptpp) REVERT: B 147 GLN cc_start: 0.8091 (tt0) cc_final: 0.7760 (tm-30) REVERT: B 186 ASN cc_start: 0.7989 (t0) cc_final: 0.7742 (t0) REVERT: C 156 PHE cc_start: 0.8524 (m-10) cc_final: 0.8246 (m-10) REVERT: C 186 PHE cc_start: 0.7260 (m-80) cc_final: 0.6731 (m-80) REVERT: C 203 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7703 (mtmt) REVERT: C 239 MET cc_start: 0.7844 (mmm) cc_final: 0.7610 (tpp) REVERT: C 385 PHE cc_start: 0.8614 (t80) cc_final: 0.8382 (t80) REVERT: C 389 PHE cc_start: 0.8563 (p90) cc_final: 0.8322 (p90) REVERT: C 407 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8262 (ttm170) REVERT: C 545 PHE cc_start: 0.7085 (t80) cc_final: 0.6818 (t80) REVERT: C 589 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8128 (t) REVERT: C 628 HIS cc_start: 0.7687 (m90) cc_final: 0.7319 (m-70) REVERT: C 954 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8930 (tptp) REVERT: C 1021 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8754 (tp) REVERT: C 1024 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8943 (mm-30) REVERT: C 1032 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8690 (ttpt) REVERT: C 1038 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: C 1304 MET cc_start: 0.8693 (tpp) cc_final: 0.8398 (tpp) REVERT: D 227 PHE cc_start: 0.8970 (t80) cc_final: 0.8617 (t80) REVERT: D 321 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8411 (tppt) REVERT: D 343 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5422 (mm) REVERT: D 398 LYS cc_start: 0.9016 (tttt) cc_final: 0.8531 (ttpp) REVERT: D 414 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7425 (tm-30) REVERT: D 495 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8672 (p0) REVERT: D 695 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8395 (tptm) REVERT: D 697 MET cc_start: 0.7576 (tpp) cc_final: 0.7319 (tmm) REVERT: D 833 GLU cc_start: 0.7950 (tp30) cc_final: 0.7638 (tp30) REVERT: D 868 TRP cc_start: 0.8364 (m-90) cc_final: 0.8093 (m-90) REVERT: D 1040 MET cc_start: 0.3254 (mtp) cc_final: 0.2640 (mmm) REVERT: E 43 ASN cc_start: 0.7760 (t0) cc_final: 0.7442 (t0) REVERT: E 67 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: M 28 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6481 (pt) REVERT: M 117 THR cc_start: 0.7679 (p) cc_final: 0.7170 (t) REVERT: M 181 ARG cc_start: 0.8590 (tmt170) cc_final: 0.8127 (tpt90) REVERT: M 203 LEU cc_start: 0.9021 (mt) cc_final: 0.8696 (tp) REVERT: M 270 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: M 456 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8258 (mmm160) outliers start: 150 outliers final: 89 residues processed: 481 average time/residue: 0.4092 time to fit residues: 307.4646 Evaluate side-chains 403 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 300 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 290 ASN Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 359 optimal weight: 30.0000 chunk 177 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 387 ASN C 526 HIS C 659 GLN C1061 GLN C1236 ASN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 430 HIS D 504 GLN ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 265 GLN ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29487 Z= 0.350 Angle : 0.700 15.076 40324 Z= 0.346 Chirality : 0.045 0.262 4762 Planarity : 0.005 0.060 5045 Dihedral : 14.468 172.741 4829 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 6.34 % Allowed : 20.49 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.13), residues: 3655 helix: 0.30 (0.15), residues: 1282 sheet: -1.44 (0.29), residues: 325 loop : -2.74 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 321 HIS 0.043 0.002 HIS A 23 PHE 0.018 0.002 PHE D 437 TYR 0.014 0.002 TYR C 92 ARG 0.005 0.001 ARG M 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 302 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8648 (mm) REVERT: B 43 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8780 (mp) REVERT: B 145 LYS cc_start: 0.8667 (ptpt) cc_final: 0.8218 (ptpp) REVERT: B 147 GLN cc_start: 0.8096 (tt0) cc_final: 0.7837 (mt0) REVERT: B 186 ASN cc_start: 0.8181 (t0) cc_final: 0.7874 (t0) REVERT: C 156 PHE cc_start: 0.8558 (m-10) cc_final: 0.8212 (m-10) REVERT: C 183 TRP cc_start: 0.8453 (m-10) cc_final: 0.8117 (m100) REVERT: C 203 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7660 (mtmm) REVERT: C 239 MET cc_start: 0.8179 (mmm) cc_final: 0.7914 (tpp) REVERT: C 385 PHE cc_start: 0.8752 (t80) cc_final: 0.8460 (t80) REVERT: C 545 PHE cc_start: 0.7168 (t80) cc_final: 0.6932 (t80) REVERT: C 589 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8259 (t) REVERT: C 628 HIS cc_start: 0.7825 (m90) cc_final: 0.7484 (m90) REVERT: C 685 MET cc_start: 0.7789 (mtm) cc_final: 0.7557 (mtt) REVERT: C 844 LYS cc_start: 0.8694 (ptpt) cc_final: 0.8451 (ptpt) REVERT: C 954 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8924 (tptp) REVERT: C 1021 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8676 (tp) REVERT: C 1024 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.9003 (mm-30) REVERT: C 1032 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8682 (ttpt) REVERT: C 1038 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8445 (tm-30) REVERT: D 321 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8481 (tppt) REVERT: D 695 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8545 (tptm) REVERT: D 697 MET cc_start: 0.7615 (tpp) cc_final: 0.7392 (tmm) REVERT: D 1040 MET cc_start: 0.3496 (mtp) cc_final: 0.2796 (mpp) REVERT: M 117 THR cc_start: 0.7608 (p) cc_final: 0.7112 (t) REVERT: M 203 LEU cc_start: 0.9037 (mt) cc_final: 0.8752 (tp) REVERT: M 236 MET cc_start: 0.8672 (mmt) cc_final: 0.8456 (mmt) REVERT: M 270 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7696 (pp20) REVERT: M 456 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8414 (mmm160) outliers start: 177 outliers final: 123 residues processed: 454 average time/residue: 0.4274 time to fit residues: 308.9097 Evaluate side-chains 408 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 273 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 40.0000 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 267 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 322 optimal weight: 0.0870 chunk 90 optimal weight: 10.0000 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 283 GLN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 560 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29487 Z= 0.295 Angle : 0.657 12.209 40324 Z= 0.325 Chirality : 0.044 0.243 4762 Planarity : 0.004 0.058 5045 Dihedral : 14.439 173.604 4825 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.54 % Favored : 91.38 % Rotamer: Outliers : 6.27 % Allowed : 21.14 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 3655 helix: 0.43 (0.15), residues: 1285 sheet: -1.28 (0.29), residues: 313 loop : -2.68 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 321 HIS 0.038 0.001 HIS D 430 PHE 0.018 0.001 PHE C 186 TYR 0.023 0.002 TYR D 144 ARG 0.010 0.001 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 289 time to evaluate : 3.482 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: A 183 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 255 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6781 (mpp-170) REVERT: B 43 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8785 (mp) REVERT: B 145 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8232 (ptpp) REVERT: B 186 ASN cc_start: 0.8218 (t0) cc_final: 0.7901 (t0) REVERT: C 156 PHE cc_start: 0.8546 (m-10) cc_final: 0.8181 (m-10) REVERT: C 183 TRP cc_start: 0.8492 (m-10) cc_final: 0.8149 (m100) REVERT: C 203 LYS cc_start: 0.8473 (mtmt) cc_final: 0.7997 (mtmt) REVERT: C 239 MET cc_start: 0.8163 (mmm) cc_final: 0.7961 (tpp) REVERT: C 385 PHE cc_start: 0.8781 (t80) cc_final: 0.8570 (t80) REVERT: C 429 MET cc_start: 0.9282 (mmp) cc_final: 0.9045 (mmp) REVERT: C 545 PHE cc_start: 0.7434 (t80) cc_final: 0.7214 (t80) REVERT: C 589 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8321 (t) REVERT: C 628 HIS cc_start: 0.7865 (m90) cc_final: 0.7503 (m90) REVERT: C 954 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8888 (tptp) REVERT: C 1021 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8658 (tp) REVERT: C 1024 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8947 (mm-30) REVERT: C 1032 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8681 (ttpt) REVERT: C 1253 LEU cc_start: 0.7592 (mt) cc_final: 0.7222 (mt) REVERT: D 159 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8523 (tp) REVERT: D 298 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8078 (mtp) REVERT: D 321 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8425 (tppt) REVERT: D 695 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8513 (tptm) REVERT: D 747 MET cc_start: 0.8201 (mmt) cc_final: 0.7910 (mmm) REVERT: D 802 ASP cc_start: 0.8243 (m-30) cc_final: 0.7990 (m-30) REVERT: D 833 GLU cc_start: 0.7919 (tp30) cc_final: 0.7629 (tp30) REVERT: D 868 TRP cc_start: 0.8557 (m-90) cc_final: 0.8242 (m-90) REVERT: D 1040 MET cc_start: 0.3769 (mtp) cc_final: 0.2641 (mmm) REVERT: M 117 THR cc_start: 0.7609 (p) cc_final: 0.7042 (t) REVERT: M 203 LEU cc_start: 0.9037 (mt) cc_final: 0.8779 (tp) REVERT: M 236 MET cc_start: 0.8685 (mmt) cc_final: 0.8423 (mmt) REVERT: M 456 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8488 (mmm160) outliers start: 175 outliers final: 128 residues processed: 435 average time/residue: 0.4064 time to fit residues: 278.7690 Evaluate side-chains 412 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 272 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1191 LYS Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.5980 chunk 323 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 211 optimal weight: 0.4980 chunk 88 optimal weight: 20.0000 chunk 359 optimal weight: 50.0000 chunk 298 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29487 Z= 0.209 Angle : 0.628 13.687 40324 Z= 0.306 Chirality : 0.042 0.227 4762 Planarity : 0.004 0.059 5045 Dihedral : 14.284 173.931 4819 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 5.73 % Allowed : 22.21 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3655 helix: 0.63 (0.15), residues: 1291 sheet: -1.23 (0.29), residues: 304 loop : -2.59 (0.12), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 321 HIS 0.007 0.001 HIS D 430 PHE 0.030 0.001 PHE C 186 TYR 0.015 0.001 TYR M 271 ARG 0.007 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 288 time to evaluate : 3.025 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 183 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 255 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6784 (mpp-170) REVERT: B 125 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8162 (ptmm) REVERT: B 137 ASN cc_start: 0.8938 (t0) cc_final: 0.8501 (t0) REVERT: B 145 LYS cc_start: 0.8569 (ptpt) cc_final: 0.8181 (ptpp) REVERT: B 186 ASN cc_start: 0.8164 (t0) cc_final: 0.7844 (t0) REVERT: C 156 PHE cc_start: 0.8525 (m-10) cc_final: 0.8171 (m-10) REVERT: C 183 TRP cc_start: 0.8536 (m-10) cc_final: 0.8230 (m100) REVERT: C 203 LYS cc_start: 0.8442 (mtmt) cc_final: 0.7977 (mtmt) REVERT: C 545 PHE cc_start: 0.7452 (t80) cc_final: 0.7227 (t80) REVERT: C 628 HIS cc_start: 0.7867 (m90) cc_final: 0.7558 (m-70) REVERT: C 954 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8784 (tptp) REVERT: C 1021 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 1024 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9023 (mm-30) REVERT: C 1032 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8674 (ttpt) REVERT: C 1161 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8249 (tt) REVERT: C 1253 LEU cc_start: 0.7639 (mt) cc_final: 0.7244 (mt) REVERT: C 1281 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8807 (m-80) REVERT: D 222 LYS cc_start: 0.9128 (mtpt) cc_final: 0.8767 (mmtm) REVERT: D 298 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: D 321 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8415 (tppt) REVERT: D 695 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8515 (tptm) REVERT: D 747 MET cc_start: 0.8189 (mmt) cc_final: 0.7955 (mmm) REVERT: D 802 ASP cc_start: 0.8278 (m-30) cc_final: 0.8022 (m-30) REVERT: D 833 GLU cc_start: 0.7869 (tp30) cc_final: 0.7610 (tp30) REVERT: D 868 TRP cc_start: 0.8484 (m-90) cc_final: 0.8217 (m-90) REVERT: D 1040 MET cc_start: 0.3796 (mtp) cc_final: 0.2559 (mmm) REVERT: D 1144 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8988 (mm) REVERT: M 117 THR cc_start: 0.7608 (p) cc_final: 0.7008 (t) REVERT: M 203 LEU cc_start: 0.9038 (mt) cc_final: 0.8786 (tp) REVERT: M 236 MET cc_start: 0.8678 (mmt) cc_final: 0.8454 (mmt) REVERT: M 270 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: M 456 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8483 (mmm160) outliers start: 160 outliers final: 128 residues processed: 422 average time/residue: 0.4026 time to fit residues: 271.5847 Evaluate side-chains 416 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 274 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1281 TYR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 302 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 165 optimal weight: 0.0980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 283 GLN C 214 ASN C 513 GLN C1256 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29487 Z= 0.291 Angle : 0.662 14.635 40324 Z= 0.325 Chirality : 0.044 0.250 4762 Planarity : 0.004 0.057 5045 Dihedral : 14.296 174.412 4817 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.84 % Favored : 91.08 % Rotamer: Outliers : 6.56 % Allowed : 21.78 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3655 helix: 0.62 (0.15), residues: 1293 sheet: -1.01 (0.30), residues: 288 loop : -2.53 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 321 HIS 0.019 0.001 HIS A 23 PHE 0.018 0.001 PHE C 186 TYR 0.013 0.001 TYR C1231 ARG 0.007 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 278 time to evaluate : 3.404 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: B 43 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8766 (mp) REVERT: B 125 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8237 (ptmm) REVERT: B 145 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8201 (ptpp) REVERT: B 147 GLN cc_start: 0.7927 (tt0) cc_final: 0.7695 (mt0) REVERT: B 186 ASN cc_start: 0.8176 (t0) cc_final: 0.7885 (t0) REVERT: C 183 TRP cc_start: 0.8581 (m-10) cc_final: 0.8293 (m100) REVERT: C 203 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8057 (mtmt) REVERT: C 545 PHE cc_start: 0.7395 (t80) cc_final: 0.7139 (t80) REVERT: C 628 HIS cc_start: 0.7839 (m90) cc_final: 0.7547 (m-70) REVERT: C 704 MET cc_start: 0.7368 (pmm) cc_final: 0.6819 (ptp) REVERT: C 954 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8829 (tptp) REVERT: C 1021 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8670 (tp) REVERT: C 1024 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9023 (mm-30) REVERT: C 1032 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8681 (ttpt) REVERT: C 1161 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8284 (tt) REVERT: C 1281 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8845 (m-80) REVERT: C 1304 MET cc_start: 0.8934 (tpp) cc_final: 0.8698 (tpp) REVERT: D 130 MET cc_start: 0.8478 (tmm) cc_final: 0.7909 (tmm) REVERT: D 222 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8798 (mmtm) REVERT: D 298 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8161 (mtp) REVERT: D 321 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8394 (tppt) REVERT: D 695 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8579 (tptm) REVERT: D 697 MET cc_start: 0.7927 (tmm) cc_final: 0.6975 (tmm) REVERT: D 868 TRP cc_start: 0.8528 (m-90) cc_final: 0.8265 (m-90) REVERT: D 1040 MET cc_start: 0.4180 (mtp) cc_final: 0.2786 (mmm) REVERT: D 1144 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8889 (mm) REVERT: E 62 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8281 (tm-30) REVERT: M 117 THR cc_start: 0.7786 (p) cc_final: 0.7143 (t) REVERT: M 236 MET cc_start: 0.8641 (mmt) cc_final: 0.8430 (mmt) REVERT: M 456 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8521 (mmm160) outliers start: 183 outliers final: 140 residues processed: 429 average time/residue: 0.4055 time to fit residues: 278.4381 Evaluate side-chains 413 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 260 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1191 LYS Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1281 TYR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 70 optimal weight: 0.0050 chunk 69 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 281 optimal weight: 50.0000 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 194 GLN C1146 GLN C1256 GLN C1314 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 29487 Z= 0.160 Angle : 0.624 12.685 40324 Z= 0.299 Chirality : 0.042 0.315 4762 Planarity : 0.004 0.056 5045 Dihedral : 14.194 174.484 4815 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 4.59 % Allowed : 23.72 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3655 helix: 0.82 (0.15), residues: 1301 sheet: -1.01 (0.29), residues: 305 loop : -2.39 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 321 HIS 0.008 0.001 HIS A 23 PHE 0.020 0.001 PHE C 186 TYR 0.019 0.001 TYR M 271 ARG 0.007 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 305 time to evaluate : 3.320 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: A 255 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6879 (mpp-170) REVERT: B 125 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8171 (ptmm) REVERT: B 145 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8168 (ptpp) REVERT: B 147 GLN cc_start: 0.7949 (tt0) cc_final: 0.7741 (mt0) REVERT: B 186 ASN cc_start: 0.8082 (t0) cc_final: 0.7805 (t0) REVERT: C 156 PHE cc_start: 0.8376 (m-10) cc_final: 0.8160 (m-10) REVERT: C 183 TRP cc_start: 0.8542 (m-10) cc_final: 0.8216 (m100) REVERT: C 203 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7505 (mtmm) REVERT: C 545 PHE cc_start: 0.7369 (t80) cc_final: 0.7097 (t80) REVERT: C 628 HIS cc_start: 0.7773 (m90) cc_final: 0.7483 (m-70) REVERT: C 704 MET cc_start: 0.7160 (pmm) cc_final: 0.6762 (ptp) REVERT: C 835 GLU cc_start: 0.7667 (pp20) cc_final: 0.7330 (pp20) REVERT: C 954 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8824 (tptp) REVERT: C 1021 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8704 (tp) REVERT: C 1024 GLU cc_start: 0.9454 (OUTLIER) cc_final: 0.9023 (mm-30) REVERT: C 1032 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8670 (ttpt) REVERT: C 1161 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8224 (tt) REVERT: C 1304 MET cc_start: 0.8811 (tpp) cc_final: 0.8481 (tpp) REVERT: D 130 MET cc_start: 0.8458 (tmm) cc_final: 0.7962 (tmm) REVERT: D 222 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8755 (mmtm) REVERT: D 298 MET cc_start: 0.8616 (tpp) cc_final: 0.8178 (mtp) REVERT: D 321 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8304 (tppt) REVERT: D 695 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8504 (tptm) REVERT: D 697 MET cc_start: 0.7884 (tmm) cc_final: 0.6935 (tmm) REVERT: D 747 MET cc_start: 0.8196 (mmt) cc_final: 0.7978 (mmm) REVERT: D 833 GLU cc_start: 0.7895 (tp30) cc_final: 0.7599 (tp30) REVERT: D 1040 MET cc_start: 0.4211 (mtp) cc_final: 0.2793 (mmm) REVERT: D 1144 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8818 (mm) REVERT: E 62 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8189 (tm-30) REVERT: M 28 LEU cc_start: 0.8335 (pp) cc_final: 0.8100 (pp) REVERT: M 117 THR cc_start: 0.7764 (p) cc_final: 0.7134 (t) REVERT: M 236 MET cc_start: 0.8635 (mmt) cc_final: 0.8433 (mmt) REVERT: M 456 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8456 (mmm160) outliers start: 128 outliers final: 92 residues processed: 412 average time/residue: 0.4061 time to fit residues: 265.5786 Evaluate side-chains 379 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 277 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 313 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 301 optimal weight: 0.0980 chunk 316 optimal weight: 0.0970 chunk 332 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 283 GLN C 214 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29487 Z= 0.228 Angle : 0.644 12.556 40324 Z= 0.313 Chirality : 0.043 0.310 4762 Planarity : 0.004 0.057 5045 Dihedral : 14.212 174.670 4813 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 4.66 % Allowed : 24.01 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3655 helix: 0.88 (0.15), residues: 1289 sheet: -0.84 (0.31), residues: 282 loop : -2.35 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 868 HIS 0.004 0.001 HIS D 364 PHE 0.023 0.001 PHE C 186 TYR 0.013 0.001 TYR C1231 ARG 0.007 0.000 ARG C 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 282 time to evaluate : 3.199 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: A 255 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6876 (mpp-170) REVERT: B 125 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8193 (ptmm) REVERT: B 145 LYS cc_start: 0.8502 (ptpt) cc_final: 0.8160 (ptpp) REVERT: B 186 ASN cc_start: 0.8126 (t0) cc_final: 0.7847 (t0) REVERT: C 156 PHE cc_start: 0.8424 (m-10) cc_final: 0.8195 (m-10) REVERT: C 183 TRP cc_start: 0.8582 (m-10) cc_final: 0.8302 (m100) REVERT: C 203 LYS cc_start: 0.8447 (mtmt) cc_final: 0.7967 (mtmt) REVERT: C 545 PHE cc_start: 0.7403 (t80) cc_final: 0.7120 (t80) REVERT: C 628 HIS cc_start: 0.7811 (m90) cc_final: 0.7530 (m-70) REVERT: C 704 MET cc_start: 0.7238 (pmm) cc_final: 0.6966 (ptp) REVERT: C 954 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8836 (tptp) REVERT: C 1021 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8712 (tp) REVERT: C 1024 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.9019 (mm-30) REVERT: C 1032 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8700 (ttpt) REVERT: C 1161 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8245 (tt) REVERT: C 1304 MET cc_start: 0.8957 (tpp) cc_final: 0.8682 (tpp) REVERT: D 130 MET cc_start: 0.8440 (tmm) cc_final: 0.7941 (tmm) REVERT: D 222 LYS cc_start: 0.9094 (mtpt) cc_final: 0.8762 (mmtm) REVERT: D 298 MET cc_start: 0.8649 (tpp) cc_final: 0.8220 (mtp) REVERT: D 321 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8351 (tppt) REVERT: D 695 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8531 (tptm) REVERT: D 697 MET cc_start: 0.7930 (tmm) cc_final: 0.6960 (tmm) REVERT: D 747 MET cc_start: 0.8289 (mmt) cc_final: 0.8004 (mmm) REVERT: D 833 GLU cc_start: 0.7873 (tp30) cc_final: 0.7554 (tp30) REVERT: D 865 HIS cc_start: 0.6560 (t70) cc_final: 0.6260 (t70) REVERT: D 1040 MET cc_start: 0.4389 (mtp) cc_final: 0.3174 (mpp) REVERT: D 1144 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8935 (mm) REVERT: E 62 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8177 (tm-30) REVERT: M 28 LEU cc_start: 0.8370 (pp) cc_final: 0.8150 (pp) REVERT: M 117 THR cc_start: 0.7797 (p) cc_final: 0.7178 (t) REVERT: M 456 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8478 (mmm160) outliers start: 130 outliers final: 99 residues processed: 390 average time/residue: 0.4048 time to fit residues: 252.8592 Evaluate side-chains 385 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 276 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 3.9990 chunk 353 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 chunk 341 optimal weight: 8.9990 chunk 295 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN C 193 ASN C 238 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29487 Z= 0.360 Angle : 0.713 13.078 40324 Z= 0.352 Chirality : 0.046 0.326 4762 Planarity : 0.005 0.057 5045 Dihedral : 14.355 174.945 4813 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.38 % Favored : 90.56 % Rotamer: Outliers : 4.37 % Allowed : 24.61 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3655 helix: 0.64 (0.15), residues: 1296 sheet: -1.03 (0.31), residues: 278 loop : -2.42 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 868 HIS 0.006 0.001 HIS D 104 PHE 0.024 0.002 PHE C 186 TYR 0.014 0.002 TYR C 26 ARG 0.009 0.001 ARG M 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 277 time to evaluate : 3.789 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: B 43 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8768 (mp) REVERT: B 125 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8166 (ptmm) REVERT: B 137 ASN cc_start: 0.8914 (t0) cc_final: 0.8616 (t0) REVERT: B 145 LYS cc_start: 0.8515 (ptpt) cc_final: 0.8288 (ptpp) REVERT: B 186 ASN cc_start: 0.8189 (t0) cc_final: 0.7892 (t0) REVERT: C 156 PHE cc_start: 0.8470 (m-10) cc_final: 0.8175 (m-10) REVERT: C 183 TRP cc_start: 0.8685 (m-10) cc_final: 0.8391 (m100) REVERT: C 203 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8098 (mtmt) REVERT: C 371 ARG cc_start: 0.5955 (ptm160) cc_final: 0.5473 (ptp-170) REVERT: C 545 PHE cc_start: 0.7544 (t80) cc_final: 0.7270 (t80) REVERT: C 628 HIS cc_start: 0.7995 (m90) cc_final: 0.7560 (m-70) REVERT: C 954 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8863 (tptp) REVERT: C 1021 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8655 (tp) REVERT: C 1024 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9126 (mm-30) REVERT: C 1032 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8702 (ttpt) REVERT: C 1161 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8325 (tt) REVERT: D 130 MET cc_start: 0.8411 (tmm) cc_final: 0.7925 (tmm) REVERT: D 222 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8811 (mmtm) REVERT: D 298 MET cc_start: 0.8678 (tpp) cc_final: 0.8234 (mtp) REVERT: D 321 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8405 (tppt) REVERT: D 643 ASP cc_start: 0.7629 (m-30) cc_final: 0.7341 (m-30) REVERT: D 695 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8552 (tptm) REVERT: D 697 MET cc_start: 0.7982 (tmm) cc_final: 0.7057 (tmm) REVERT: D 747 MET cc_start: 0.8285 (mmt) cc_final: 0.8014 (mmm) REVERT: D 833 GLU cc_start: 0.7847 (tp30) cc_final: 0.7533 (tp30) REVERT: D 1040 MET cc_start: 0.4515 (mtp) cc_final: 0.3297 (mpp) REVERT: D 1143 ASP cc_start: 0.7200 (m-30) cc_final: 0.6884 (t0) REVERT: D 1144 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8921 (mm) REVERT: E 62 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8132 (tm-30) REVERT: M 28 LEU cc_start: 0.8401 (pp) cc_final: 0.8180 (pp) REVERT: M 117 THR cc_start: 0.7847 (p) cc_final: 0.7207 (t) REVERT: M 288 GLU cc_start: 0.8030 (tp30) cc_final: 0.7788 (mm-30) REVERT: M 456 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8475 (mmm160) outliers start: 122 outliers final: 103 residues processed: 378 average time/residue: 0.4279 time to fit residues: 256.5512 Evaluate side-chains 376 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 262 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 408 ASN Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 43 optimal weight: 30.0000 chunk 82 optimal weight: 0.0040 chunk 295 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 194 GLN C 214 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.140412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087469 restraints weight = 57700.381| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.18 r_work: 0.3032 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 29487 Z= 0.343 Angle : 0.840 59.199 40324 Z= 0.438 Chirality : 0.045 0.637 4762 Planarity : 0.005 0.057 5045 Dihedral : 14.355 174.949 4812 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.41 % Favored : 90.53 % Rotamer: Outliers : 4.44 % Allowed : 24.47 % Favored : 71.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3655 helix: 0.64 (0.15), residues: 1296 sheet: -1.04 (0.31), residues: 278 loop : -2.42 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 868 HIS 0.006 0.001 HIS A 23 PHE 0.022 0.001 PHE C 186 TYR 0.014 0.001 TYR C 26 ARG 0.005 0.000 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7279.92 seconds wall clock time: 130 minutes 29.30 seconds (7829.30 seconds total)