Starting phenix.real_space_refine on Mon Feb 19 22:01:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9g_4770/02_2024/6r9g_4770.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9g_4770/02_2024/6r9g_4770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9g_4770/02_2024/6r9g_4770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9g_4770/02_2024/6r9g_4770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9g_4770/02_2024/6r9g_4770.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r9g_4770/02_2024/6r9g_4770.pdb" } resolution = 3.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 16236 2.51 5 N 4498 2.21 5 O 5107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 720": "NH1" <-> "NH2" Residue "C PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1142": "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 "C ARG 1301": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 709": "NH1" <-> "NH2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 836": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 933": "NH1" <-> "NH2" Residue "D ARG 978": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1067": "NH1" <-> "NH2" Residue "D ARG 1075": "NH1" <-> "NH2" Residue "D ARG 1123": "NH1" <-> "NH2" Residue "D ARG 1173": "NH1" <-> "NH2" Residue "D ARG 1174": "NH1" <-> "NH2" Residue "D ASP 1181": "OD1" <-> "OD2" Residue "D ARG 1203": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "D ARG 1373": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25944 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1765 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 220} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1743 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 221} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10112 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'TYR:plan': 6, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 309 Chain: "D" Number of atoms: 10051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10051 Classifications: {'peptide': 1334} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 65} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1280} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 10, 'GLU:plan': 3, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 220 Chain: "E" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 849 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 101} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 852 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 3} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 14.27, per 1000 atoms: 0.55 Number of scatterers: 25944 At special positions: 0 Unit cell: (141.37, 167.745, 152.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 5107 8.00 N 4498 7.00 C 16236 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: 8.90 Conformation dependent library (CDL) restraints added in 4.8 seconds 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6342 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 28 sheets defined 36.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.512A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.597A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.778A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.016A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.791A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.751A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.358A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.688A pdb=" N GLY C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.905A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.611A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.514A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.842A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.613A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 4.125A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 4.168A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.333A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 899 through 907 removed outlier: 3.626A pdb=" N GLY C 907 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 979 removed outlier: 6.265A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 992 through 1000 removed outlier: 4.216A pdb=" N ARG C 996 " --> pdb=" O LEU C 992 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 removed outlier: 3.552A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.782A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1120 " --> pdb=" O HIS C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.587A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1176 removed outlier: 3.651A pdb=" N LEU C1172 " --> pdb=" O GLU C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1200 Processing helix chain 'C' and resid 1201 through 1203 No H-bonds generated for 'chain 'C' and resid 1201 through 1203' Processing helix chain 'C' and resid 1273 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 3.661A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1331 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.510A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 182 through 192 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.064A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 285 removed outlier: 4.274A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.769A pdb=" N MET D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.917A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) 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 417 removed outlier: 3.514A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) 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 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.815A pdb=" N LEU D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.800A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.699A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.689A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 674 through 701 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.005A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 784 removed outlier: 4.297A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA D 784 " --> pdb=" O ARG D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.117A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 916 through 925 removed outlier: 3.673A pdb=" N GLN D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.581A pdb=" N ALA D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D1147 " --> pdb=" O ASP D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.911A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.373A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 4.261A pdb=" N GLU D1293 " --> pdb=" O ASN D1289 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1322 removed outlier: 3.580A pdb=" N ALA D1322 " --> pdb=" O PHE D1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.542A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 3.939A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.293A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.538A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'G' and resid 6 through 26 removed outlier: 3.501A pdb=" N VAL G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 33 through 43 removed outlier: 3.954A pdb=" N HIS G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.803A pdb=" N VAL G 55 " --> pdb=" O ASP G 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 57 " --> pdb=" O PHE G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 108 removed outlier: 4.045A pdb=" N GLU G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL G 108 " --> pdb=" O TYR G 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 76 through 105 removed outlier: 3.966A pdb=" N ILE F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 5.206A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.635A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (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 17 through 18 removed outlier: 4.222A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 60 removed outlier: 3.714A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 57 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.480A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 69 removed outlier: 4.257A pdb=" N GLN C 69 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 101 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 94 through 98 removed outlier: 5.127A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.926A pdb=" N PHE C 136 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.483A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AB3, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.698A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.869A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.656A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.514A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 724 through 727 removed outlier: 5.485A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR C 726 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC1, first strand: chain 'C' and resid 817 through 818 removed outlier: 8.605A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 830 through 837 removed outlier: 3.930A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 105 through 112 removed outlier: 11.646A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 355 through 357 Processing sheet with id=AC5, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.740A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 434 through 437 Processing sheet with id=AC7, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.624A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 821 through 822 removed outlier: 3.558A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.513A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 1264 through 1265 895 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.64 Time building geometry restraints manager: 9.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8335 1.34 - 1.46: 3224 1.46 - 1.57: 14567 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 26306 Sorted by residual: bond pdb=" C GLU D 925 " pdb=" N PRO D 926 " ideal model delta sigma weight residual 1.332 1.395 -0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.51e+00 bond pdb=" CA PHE D1165 " pdb=" C PHE D1165 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.32e-02 5.74e+03 4.47e+00 bond pdb=" CA ILE D 416 " pdb=" C ILE D 416 " ideal model delta sigma weight residual 1.519 1.543 -0.024 1.14e-02 7.69e+03 4.43e+00 bond pdb=" C LYS C 496 " pdb=" N PRO C 497 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.23e-02 6.61e+03 3.18e+00 ... (remaining 26301 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.20: 670 106.20 - 113.57: 14631 113.57 - 120.94: 12092 120.94 - 128.31: 8163 128.31 - 135.68: 121 Bond angle restraints: 35677 Sorted by residual: angle pdb=" N VAL D 885 " pdb=" CA VAL D 885 " pdb=" C VAL D 885 " ideal model delta sigma weight residual 109.34 122.65 -13.31 2.08e+00 2.31e-01 4.09e+01 angle pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" C GLU B 29 " ideal model delta sigma weight residual 109.81 121.95 -12.14 2.21e+00 2.05e-01 3.02e+01 angle pdb=" C ASP F 25 " pdb=" N ASP F 26 " pdb=" CA ASP F 26 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C ARG D 933 " pdb=" N THR D 934 " pdb=" CA THR D 934 " ideal model delta sigma weight residual 122.61 130.23 -7.62 1.56e+00 4.11e-01 2.38e+01 angle pdb=" N LEU D 127 " pdb=" CA LEU D 127 " pdb=" C LEU D 127 " ideal model delta sigma weight residual 110.30 117.61 -7.31 1.50e+00 4.44e-01 2.37e+01 ... (remaining 35672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 15346 15.22 - 30.44: 576 30.44 - 45.65: 173 45.65 - 60.87: 14 60.87 - 76.09: 21 Dihedral angle restraints: 16130 sinusoidal: 6293 harmonic: 9837 Sorted by residual: dihedral pdb=" C GLU B 29 " pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " ideal model delta harmonic sigma weight residual -122.60 -147.50 24.90 0 2.50e+00 1.60e-01 9.92e+01 dihedral pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " ideal model delta harmonic sigma weight residual 122.80 146.60 -23.80 0 2.50e+00 1.60e-01 9.06e+01 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 0.00 -29.45 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 16127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 4162 0.216 - 0.431: 17 0.431 - 0.647: 0 0.647 - 0.862: 0 0.862 - 1.078: 1 Chirality restraints: 4180 Sorted by residual: chirality pdb=" CA GLU B 29 " pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CB GLU B 29 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA LEU C1176 " pdb=" N LEU C1176 " pdb=" C LEU C1176 " pdb=" CB LEU C1176 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA LEU C 571 " pdb=" N LEU C 571 " pdb=" C LEU C 571 " pdb=" CB LEU C 571 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4177 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D1164 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.32e+00 pdb=" C SER D1164 " -0.050 2.00e-02 2.50e+03 pdb=" O SER D1164 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE D1165 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 488 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO C 489 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 489 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 489 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C1064 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C ASP C1064 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP C1064 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C1065 " -0.015 2.00e-02 2.50e+03 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7447 2.83 - 3.34: 22492 3.34 - 3.86: 39588 3.86 - 4.38: 43256 4.38 - 4.90: 75915 Nonbonded interactions: 188698 Sorted by model distance: nonbonded pdb=" OE1 GLN C 148 " pdb=" OG SER C 531 " model vdw 2.307 2.440 nonbonded pdb=" OG SER D1160 " pdb=" O VAL D1204 " model vdw 2.325 2.440 nonbonded pdb=" OH TYR C 123 " pdb=" OE2 GLU C 126 " model vdw 2.328 2.440 nonbonded pdb=" O LYS C1328 " pdb=" OG SER C1332 " model vdw 2.335 2.440 nonbonded pdb=" OH TYR C1281 " pdb=" O ILE D 434 " model vdw 2.336 2.440 ... (remaining 188693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 70 or (resid 71 and (name N or name \ CA or name C or name O or name CB )) or resid 72 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 142 or (resid 143 and (name N or name CA or name C or name O or name C \ B )) or resid 144 through 163 or (resid 164 and (name N or name CA or name C or \ name O or name CB )) or resid 165 or (resid 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N or n \ ame CA or name C or name O or name CB )) or resid 171 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 23 \ 5)) selection = (chain 'B' and (resid 6 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161 through 190 or (resid 191 a \ nd (name N or name CA or name C or name O or name CB )) or resid 192 through 235 \ )) } ncs_group { reference = (chain 'F' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 108)) selection = (chain 'G' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 23 or (resid 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 85 or (resid 86 and (name N or na \ me CA or name C or name O or name CB )) or resid 87 through 108)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 4.900 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 66.220 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26306 Z= 0.221 Angle : 0.868 13.310 35677 Z= 0.491 Chirality : 0.055 1.078 4180 Planarity : 0.006 0.066 4716 Dihedral : 9.851 76.091 9788 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.97 % Favored : 91.91 % Rotamer: Outliers : 0.33 % Allowed : 2.64 % Favored : 97.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.26 % 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: -4.32 (0.11), residues: 3399 helix: -2.71 (0.10), residues: 1162 sheet: -1.22 (0.31), residues: 237 loop : -3.34 (0.11), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 236 HIS 0.007 0.001 HIS F 34 PHE 0.028 0.002 PHE D 227 TYR 0.032 0.002 TYR D 360 ARG 0.005 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 788 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8073 (tt) cc_final: 0.7708 (pt) REVERT: B 219 ARG cc_start: 0.6456 (mtp-110) cc_final: 0.5820 (ttt180) REVERT: C 40 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6160 (tp30) REVERT: C 685 MET cc_start: 0.5744 (mmp) cc_final: 0.5541 (mmp) REVERT: C 878 THR cc_start: 0.7393 (p) cc_final: 0.6965 (p) REVERT: C 1069 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6869 (mtm110) REVERT: D 17 PHE cc_start: 0.3209 (t80) cc_final: 0.1825 (t80) REVERT: D 240 THR cc_start: 0.8828 (m) cc_final: 0.8588 (p) REVERT: D 349 TYR cc_start: 0.3922 (m-80) cc_final: 0.3683 (m-80) REVERT: D 485 MET cc_start: 0.5412 (mmm) cc_final: 0.4573 (mmt) REVERT: D 634 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7184 (mtt-85) REVERT: D 661 VAL cc_start: 0.6476 (t) cc_final: 0.5970 (t) REVERT: G 52 ILE cc_start: 0.5767 (mt) cc_final: 0.5472 (mm) REVERT: F 17 MET cc_start: 0.7418 (mmm) cc_final: 0.6259 (ppp) REVERT: F 39 MET cc_start: 0.7336 (mmm) cc_final: 0.6895 (mmp) REVERT: F 53 PHE cc_start: 0.7446 (m-80) cc_final: 0.7199 (m-80) outliers start: 9 outliers final: 1 residues processed: 793 average time/residue: 0.4508 time to fit residues: 527.1878 Evaluate side-chains 424 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 40.0000 chunk 257 optimal weight: 0.0010 chunk 142 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 128 HIS ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 69 GLN C 165 HIS C 339 ASN C 437 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C 725 GLN C 808 ASN C 965 GLN C1220 GLN ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS C1288 GLN D 186 GLN D 196 GLN D 209 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN D 435 GLN D 448 GLN D 504 GLN D 700 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 HIS ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1268 ASN G 8 ASN F 34 HIS F 82 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26306 Z= 0.340 Angle : 0.787 12.868 35677 Z= 0.404 Chirality : 0.048 0.295 4180 Planarity : 0.006 0.072 4716 Dihedral : 5.327 53.435 3687 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.18 % Favored : 91.67 % Rotamer: Outliers : 3.56 % Allowed : 11.77 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -3.02 (0.12), residues: 3399 helix: -0.99 (0.13), residues: 1175 sheet: -1.33 (0.31), residues: 247 loop : -2.89 (0.12), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 236 HIS 0.014 0.002 HIS C 554 PHE 0.025 0.003 PHE C 828 TYR 0.023 0.003 TYR G 48 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 443 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8165 (tt) cc_final: 0.7586 (pt) REVERT: C 40 GLU cc_start: 0.6532 (tm-30) cc_final: 0.6289 (tp30) REVERT: C 407 ARG cc_start: 0.8311 (mmm160) cc_final: 0.7579 (mmt180) REVERT: C 463 GLN cc_start: 0.7178 (tp-100) cc_final: 0.6939 (tm-30) REVERT: C 533 LEU cc_start: 0.7759 (mt) cc_final: 0.7329 (pt) REVERT: C 654 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.5471 (m-30) REVERT: C 685 MET cc_start: 0.6442 (mmp) cc_final: 0.6232 (mmt) REVERT: C 813 GLU cc_start: 0.5257 (mm-30) cc_final: 0.4872 (mm-30) REVERT: C 965 GLN cc_start: 0.8260 (mt0) cc_final: 0.7724 (pt0) REVERT: C 1107 MET cc_start: 0.7693 (mmt) cc_final: 0.7452 (mmt) REVERT: C 1108 ASN cc_start: 0.6892 (p0) cc_final: 0.6661 (m-40) REVERT: C 1119 MET cc_start: 0.7679 (tpt) cc_final: 0.7468 (tpt) REVERT: C 1180 MET cc_start: 0.7513 (tpp) cc_final: 0.7130 (tpp) REVERT: C 1198 LEU cc_start: 0.8004 (tp) cc_final: 0.7656 (tt) REVERT: D 17 PHE cc_start: 0.2792 (t80) cc_final: 0.1613 (t80) REVERT: D 349 TYR cc_start: 0.4545 (m-80) cc_final: 0.4005 (m-80) REVERT: D 445 LYS cc_start: 0.5434 (OUTLIER) cc_final: 0.4977 (mmmt) REVERT: D 698 MET cc_start: 0.5242 (mmm) cc_final: 0.4189 (mmm) REVERT: D 817 HIS cc_start: 0.7366 (t70) cc_final: 0.7041 (t-90) REVERT: D 1349 GLU cc_start: 0.6044 (tt0) cc_final: 0.4626 (mp0) REVERT: G 52 ILE cc_start: 0.6243 (mt) cc_final: 0.5963 (mm) REVERT: G 94 TRP cc_start: 0.8034 (t-100) cc_final: 0.7787 (t-100) REVERT: F 17 MET cc_start: 0.7839 (mmm) cc_final: 0.6716 (mtp) REVERT: F 39 MET cc_start: 0.6299 (mmm) cc_final: 0.6081 (mmt) outliers start: 97 outliers final: 48 residues processed: 507 average time/residue: 0.4111 time to fit residues: 325.8616 Evaluate side-chains 372 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 322 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 309 optimal weight: 0.9990 chunk 334 optimal weight: 7.9990 chunk 275 optimal weight: 0.9980 chunk 306 optimal weight: 0.0370 chunk 105 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 overall best weight: 1.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C 618 GLN C 808 ASN C1072 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26306 Z= 0.237 Angle : 0.658 13.438 35677 Z= 0.333 Chirality : 0.044 0.276 4180 Planarity : 0.005 0.112 4716 Dihedral : 4.956 54.524 3687 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.71 % Favored : 92.20 % Rotamer: Outliers : 3.59 % Allowed : 14.48 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.41 (0.13), residues: 3399 helix: -0.26 (0.14), residues: 1178 sheet: -0.97 (0.31), residues: 264 loop : -2.69 (0.12), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 580 HIS 0.008 0.001 HIS C 554 PHE 0.024 0.002 PHE D 172 TYR 0.019 0.001 TYR A 177 ARG 0.014 0.001 ARG D 860 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 344 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7259 (pt0) cc_final: 0.6620 (mt-10) REVERT: A 99 ILE cc_start: 0.8163 (tt) cc_final: 0.7568 (pt) REVERT: A 131 CYS cc_start: 0.5475 (OUTLIER) cc_final: 0.4684 (p) REVERT: B 219 ARG cc_start: 0.6879 (mtp-110) cc_final: 0.6480 (ttp-170) REVERT: C 40 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6477 (tp30) REVERT: C 407 ARG cc_start: 0.8335 (mmm160) cc_final: 0.7541 (mmt180) REVERT: C 533 LEU cc_start: 0.7760 (mt) cc_final: 0.7324 (pt) REVERT: C 629 PHE cc_start: 0.3233 (OUTLIER) cc_final: 0.2202 (t80) REVERT: C 710 VAL cc_start: 0.7183 (p) cc_final: 0.6970 (m) REVERT: C 813 GLU cc_start: 0.5429 (mm-30) cc_final: 0.4866 (mm-30) REVERT: C 1180 MET cc_start: 0.7443 (tpp) cc_final: 0.6885 (tpp) REVERT: C 1198 LEU cc_start: 0.8085 (tp) cc_final: 0.7745 (tt) REVERT: D 17 PHE cc_start: 0.2900 (t80) cc_final: 0.2019 (t80) REVERT: D 361 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5702 (mt) REVERT: D 445 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4896 (mmmt) REVERT: D 491 LEU cc_start: 0.7019 (mt) cc_final: 0.6649 (mp) REVERT: D 534 GLU cc_start: 0.6320 (pt0) cc_final: 0.6067 (mm-30) REVERT: D 798 ARG cc_start: 0.7230 (mtp85) cc_final: 0.6677 (mtp85) REVERT: D 817 HIS cc_start: 0.7253 (t70) cc_final: 0.6958 (t-90) REVERT: D 821 MET cc_start: 0.8253 (tpp) cc_final: 0.7966 (mmm) REVERT: D 1349 GLU cc_start: 0.6244 (tt0) cc_final: 0.5032 (mp0) REVERT: G 5 MET cc_start: 0.4561 (ppp) cc_final: 0.4021 (ppp) REVERT: G 17 MET cc_start: 0.6689 (ptm) cc_final: 0.5997 (ptm) REVERT: G 52 ILE cc_start: 0.6183 (mt) cc_final: 0.5796 (mm) REVERT: G 64 GLU cc_start: 0.6755 (mp0) cc_final: 0.6322 (pp20) REVERT: F 16 GLU cc_start: 0.7255 (tp30) cc_final: 0.7050 (tp30) REVERT: F 17 MET cc_start: 0.7775 (mmm) cc_final: 0.6050 (ppp) REVERT: F 39 MET cc_start: 0.6571 (mmm) cc_final: 0.6199 (mmt) outliers start: 98 outliers final: 60 residues processed: 415 average time/residue: 0.3688 time to fit residues: 243.3055 Evaluate side-chains 378 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1282 TYR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 310 optimal weight: 0.9990 chunk 328 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 206 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN D1259 GLN D1367 GLN G 21 ASN F 82 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 26306 Z= 0.531 Angle : 0.947 15.695 35677 Z= 0.483 Chirality : 0.054 0.334 4180 Planarity : 0.007 0.085 4716 Dihedral : 6.129 31.166 3687 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.65 % Favored : 89.11 % Rotamer: Outliers : 5.43 % Allowed : 15.43 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.68 (0.13), residues: 3399 helix: -0.60 (0.14), residues: 1203 sheet: -1.15 (0.32), residues: 259 loop : -2.80 (0.12), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 94 HIS 0.018 0.002 HIS C 554 PHE 0.043 0.004 PHE C 828 TYR 0.042 0.003 TYR C 26 ARG 0.010 0.001 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 360 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8317 (tt) cc_final: 0.7656 (pt) REVERT: A 127 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6881 (tm-30) REVERT: C 40 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6691 (tp30) REVERT: C 135 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7237 (t) REVERT: C 136 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7397 (p90) REVERT: C 138 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6826 (mp) REVERT: C 407 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8223 (mmm160) REVERT: C 629 PHE cc_start: 0.3598 (OUTLIER) cc_final: 0.2584 (t80) REVERT: C 681 MET cc_start: 0.6011 (ttm) cc_final: 0.5537 (ttm) REVERT: C 685 MET cc_start: 0.6520 (mmt) cc_final: 0.6277 (mmt) REVERT: C 799 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.5728 (p0) REVERT: C 811 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8059 (p0) REVERT: C 1072 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7395 (m-40) REVERT: C 1107 MET cc_start: 0.7471 (mmt) cc_final: 0.7014 (mmt) REVERT: C 1198 LEU cc_start: 0.8320 (tp) cc_final: 0.7957 (tt) REVERT: D 236 TRP cc_start: 0.7645 (OUTLIER) cc_final: 0.7000 (m100) REVERT: D 361 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6047 (mt) REVERT: D 491 LEU cc_start: 0.7773 (mt) cc_final: 0.7445 (mp) REVERT: D 1263 LYS cc_start: 0.4900 (tptp) cc_final: 0.4119 (mtmt) REVERT: D 1349 GLU cc_start: 0.6533 (tt0) cc_final: 0.5101 (mp0) REVERT: G 5 MET cc_start: 0.4646 (ppp) cc_final: 0.4162 (ppp) REVERT: G 17 MET cc_start: 0.6244 (ptm) cc_final: 0.5986 (ptm) REVERT: G 52 ILE cc_start: 0.6188 (mt) cc_final: 0.5764 (mm) REVERT: G 64 GLU cc_start: 0.6868 (mp0) cc_final: 0.6305 (pp20) REVERT: F 17 MET cc_start: 0.7970 (mmm) cc_final: 0.6143 (ppp) REVERT: F 39 MET cc_start: 0.6640 (mmm) cc_final: 0.6143 (mmt) REVERT: F 91 ILE cc_start: 0.7414 (mm) cc_final: 0.6777 (pt) outliers start: 148 outliers final: 91 residues processed: 470 average time/residue: 0.3851 time to fit residues: 284.6824 Evaluate side-chains 408 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 308 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 50.0000 chunk 186 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 280 optimal weight: 30.0000 chunk 227 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 167 optimal weight: 0.6980 chunk 294 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1264 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1249 ASN F 47 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26306 Z= 0.293 Angle : 0.722 12.607 35677 Z= 0.365 Chirality : 0.046 0.300 4180 Planarity : 0.005 0.053 4716 Dihedral : 5.457 29.074 3685 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.12 % Favored : 90.82 % Rotamer: Outliers : 4.29 % Allowed : 18.22 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.31 (0.13), residues: 3399 helix: -0.12 (0.15), residues: 1200 sheet: -1.33 (0.31), residues: 262 loop : -2.62 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 580 HIS 0.011 0.001 HIS C1313 PHE 0.023 0.002 PHE C 828 TYR 0.024 0.002 TYR A 177 ARG 0.011 0.001 ARG C 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 326 time to evaluate : 3.257 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 99 ILE cc_start: 0.8328 (tt) cc_final: 0.7637 (pt) REVERT: C 24 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7136 (p) REVERT: C 40 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6695 (tp30) REVERT: C 136 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7462 (p90) REVERT: C 407 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8251 (mmm160) REVERT: C 629 PHE cc_start: 0.3779 (OUTLIER) cc_final: 0.2939 (t80) REVERT: C 681 MET cc_start: 0.5850 (ttm) cc_final: 0.5565 (ttm) REVERT: C 782 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8692 (t) REVERT: C 1198 LEU cc_start: 0.8198 (tp) cc_final: 0.7606 (tt) REVERT: C 1243 MET cc_start: 0.6390 (tpt) cc_final: 0.6176 (tpt) REVERT: D 130 MET cc_start: 0.4658 (pmm) cc_final: 0.4411 (pmm) REVERT: D 361 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5906 (mt) REVERT: D 472 LEU cc_start: 0.8791 (mt) cc_final: 0.8549 (mm) REVERT: D 491 LEU cc_start: 0.7799 (mt) cc_final: 0.7577 (mp) REVERT: D 743 MET cc_start: 0.7086 (mmm) cc_final: 0.6573 (mmm) REVERT: D 798 ARG cc_start: 0.7434 (mtp85) cc_final: 0.6990 (mtp85) REVERT: D 1263 LYS cc_start: 0.4453 (tptp) cc_final: 0.3836 (mttp) REVERT: D 1349 GLU cc_start: 0.6491 (tt0) cc_final: 0.5136 (mp0) REVERT: E 1 MET cc_start: -0.0679 (ppp) cc_final: -0.1002 (ptm) REVERT: G 5 MET cc_start: 0.4778 (ppp) cc_final: 0.4433 (ppp) REVERT: G 52 ILE cc_start: 0.6152 (mt) cc_final: 0.5746 (mm) REVERT: G 62 ASP cc_start: 0.6904 (m-30) cc_final: 0.6624 (m-30) REVERT: G 64 GLU cc_start: 0.6862 (mp0) cc_final: 0.6313 (pp20) REVERT: F 17 MET cc_start: 0.7863 (mmm) cc_final: 0.6173 (ppp) REVERT: F 91 ILE cc_start: 0.7370 (mm) cc_final: 0.6768 (pt) outliers start: 117 outliers final: 78 residues processed: 414 average time/residue: 0.3791 time to fit residues: 248.0467 Evaluate side-chains 374 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 291 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 8.9990 chunk 295 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 328 optimal weight: 9.9990 chunk 273 optimal weight: 40.0000 chunk 152 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 overall best weight: 9.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN C1256 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.8331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.173 26306 Z= 0.798 Angle : 1.132 18.901 35677 Z= 0.586 Chirality : 0.062 0.376 4180 Planarity : 0.009 0.101 4716 Dihedral : 7.179 35.501 3685 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 30.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.00 % Favored : 86.73 % Rotamer: Outliers : 6.85 % Allowed : 18.66 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.15 (0.13), residues: 3399 helix: -1.15 (0.14), residues: 1204 sheet: -1.51 (0.32), residues: 262 loop : -2.93 (0.12), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 115 HIS 0.026 0.003 HIS C1116 PHE 0.041 0.004 PHE C 828 TYR 0.043 0.004 TYR C 26 ARG 0.037 0.001 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 312 time to evaluate : 3.339 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 99 ILE cc_start: 0.8451 (tt) cc_final: 0.7795 (pt) REVERT: C 24 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7502 (p) REVERT: C 136 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7525 (p90) REVERT: C 138 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7117 (mp) REVERT: C 407 ARG cc_start: 0.8571 (mmm160) cc_final: 0.8313 (mmm160) REVERT: C 629 PHE cc_start: 0.4606 (OUTLIER) cc_final: 0.3955 (t80) REVERT: C 681 MET cc_start: 0.6104 (ttm) cc_final: 0.5826 (ttm) REVERT: C 685 MET cc_start: 0.6815 (mmt) cc_final: 0.6523 (mmt) REVERT: C 755 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8734 (tppt) REVERT: C 974 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7837 (mtm-85) REVERT: C 1107 MET cc_start: 0.7502 (mmt) cc_final: 0.7143 (mtp) REVERT: C 1198 LEU cc_start: 0.8321 (tp) cc_final: 0.8063 (tt) REVERT: C 1216 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6688 (ttp-170) REVERT: C 1238 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6996 (mt) REVERT: D 130 MET cc_start: 0.5142 (pmm) cc_final: 0.4909 (pmm) REVERT: D 180 MET cc_start: 0.6145 (tpt) cc_final: 0.5631 (tpt) REVERT: D 269 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7466 (t80) REVERT: D 281 ARG cc_start: 0.8468 (mmm160) cc_final: 0.8035 (mmm160) REVERT: D 361 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6361 (mt) REVERT: D 417 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.3979 (ttp80) REVERT: D 448 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7387 (mm-40) REVERT: D 477 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: D 837 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8317 (p0) REVERT: D 1263 LYS cc_start: 0.4939 (tptp) cc_final: 0.4501 (mttm) REVERT: D 1349 GLU cc_start: 0.7008 (tt0) cc_final: 0.5256 (mp0) REVERT: G 62 ASP cc_start: 0.7018 (m-30) cc_final: 0.6683 (m-30) outliers start: 187 outliers final: 124 residues processed: 456 average time/residue: 0.4115 time to fit residues: 299.2998 Evaluate side-chains 415 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 278 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1169 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 417 ARG Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 477 GLN Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1272 SER Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 240 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 276 optimal weight: 30.0000 chunk 183 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 205 optimal weight: 0.3980 chunk 199 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 688 GLN C 965 GLN C1072 ASN C1256 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN D1367 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26306 Z= 0.213 Angle : 0.725 14.288 35677 Z= 0.370 Chirality : 0.046 0.248 4180 Planarity : 0.005 0.060 4716 Dihedral : 5.621 35.044 3685 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.30 % Favored : 91.64 % Rotamer: Outliers : 3.56 % Allowed : 21.77 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.29 (0.14), residues: 3399 helix: -0.15 (0.14), residues: 1203 sheet: -1.29 (0.32), residues: 244 loop : -2.58 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 580 HIS 0.013 0.001 HIS G 38 PHE 0.043 0.002 PHE C 156 TYR 0.028 0.002 TYR A 177 ARG 0.008 0.001 ARG D 860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 333 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8352 (tt) cc_final: 0.7666 (pt) REVERT: C 24 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7564 (p) REVERT: C 136 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.6377 (p90) REVERT: C 138 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7064 (mp) REVERT: C 407 ARG cc_start: 0.8712 (mmm160) cc_final: 0.8290 (mmm160) REVERT: C 573 ASN cc_start: 0.6827 (m-40) cc_final: 0.6594 (m-40) REVERT: C 685 MET cc_start: 0.6436 (mmt) cc_final: 0.6211 (mmt) REVERT: C 808 ASN cc_start: 0.8290 (t0) cc_final: 0.8025 (t0) REVERT: C 958 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7810 (tttt) REVERT: C 965 GLN cc_start: 0.8078 (mt0) cc_final: 0.7779 (pt0) REVERT: C 974 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: C 1107 MET cc_start: 0.7593 (mmt) cc_final: 0.7082 (mmt) REVERT: C 1198 LEU cc_start: 0.7968 (tp) cc_final: 0.7337 (tt) REVERT: C 1287 LEU cc_start: 0.6259 (tp) cc_final: 0.4966 (tt) REVERT: D 743 MET cc_start: 0.6988 (mmm) cc_final: 0.6783 (mmm) REVERT: D 798 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7094 (mtp85) REVERT: D 1349 GLU cc_start: 0.6331 (tt0) cc_final: 0.5149 (mp0) REVERT: G 5 MET cc_start: 0.4834 (ppp) cc_final: 0.4356 (ppp) REVERT: G 64 GLU cc_start: 0.6845 (pm20) cc_final: 0.6283 (pm20) REVERT: F 17 MET cc_start: 0.7490 (mmm) cc_final: 0.5921 (ptm) REVERT: F 33 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5495 (pp) REVERT: F 39 MET cc_start: 0.6620 (tpp) cc_final: 0.6089 (tpp) REVERT: F 91 ILE cc_start: 0.7235 (mm) cc_final: 0.6562 (pt) outliers start: 97 outliers final: 55 residues processed: 403 average time/residue: 0.3547 time to fit residues: 227.4280 Evaluate side-chains 355 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 296 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain G residue 47 HIS Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 195 optimal weight: 7.9990 chunk 98 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 223 optimal weight: 0.1980 chunk 162 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 554 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.8193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 26306 Z= 0.327 Angle : 0.765 13.900 35677 Z= 0.389 Chirality : 0.048 0.265 4180 Planarity : 0.005 0.056 4716 Dihedral : 5.698 30.712 3685 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.86 % Favored : 89.06 % Rotamer: Outliers : 4.25 % Allowed : 22.21 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.26 (0.14), residues: 3399 helix: -0.13 (0.14), residues: 1209 sheet: -1.37 (0.32), residues: 242 loop : -2.56 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 580 HIS 0.009 0.002 HIS C 554 PHE 0.036 0.002 PHE C 156 TYR 0.026 0.002 TYR A 177 ARG 0.016 0.001 ARG D 860 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 310 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8371 (tt) cc_final: 0.7673 (pt) REVERT: B 205 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6907 (tmm) REVERT: C 24 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7644 (p) REVERT: C 136 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7302 (p90) REVERT: C 138 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7176 (mp) REVERT: C 407 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8294 (mmm160) REVERT: C 629 PHE cc_start: 0.3965 (OUTLIER) cc_final: 0.3147 (t80) REVERT: C 685 MET cc_start: 0.6482 (mmt) cc_final: 0.6064 (mmt) REVERT: C 755 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8638 (tppt) REVERT: C 958 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7854 (tttt) REVERT: C 965 GLN cc_start: 0.8186 (mt0) cc_final: 0.7805 (pt0) REVERT: C 1107 MET cc_start: 0.7492 (mmt) cc_final: 0.6913 (mtp) REVERT: C 1198 LEU cc_start: 0.7990 (tp) cc_final: 0.7364 (tt) REVERT: D 743 MET cc_start: 0.7177 (mmm) cc_final: 0.6691 (mmp) REVERT: D 798 ARG cc_start: 0.7492 (mtp85) cc_final: 0.7219 (mtp85) REVERT: D 1263 LYS cc_start: 0.4527 (tptp) cc_final: 0.3620 (mtmt) REVERT: D 1349 GLU cc_start: 0.6576 (tt0) cc_final: 0.5161 (mp0) REVERT: G 5 MET cc_start: 0.4945 (ppp) cc_final: 0.4452 (ppp) REVERT: G 64 GLU cc_start: 0.6802 (pm20) cc_final: 0.6126 (pm20) REVERT: F 17 MET cc_start: 0.7547 (mmm) cc_final: 0.5974 (ptm) REVERT: F 33 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5469 (pp) REVERT: F 39 MET cc_start: 0.6577 (tpp) cc_final: 0.6162 (tpp) outliers start: 116 outliers final: 88 residues processed: 394 average time/residue: 0.3792 time to fit residues: 235.4400 Evaluate side-chains 396 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 301 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 286 optimal weight: 0.0570 chunk 305 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 275 optimal weight: 0.6980 chunk 288 optimal weight: 50.0000 chunk 304 optimal weight: 5.9990 overall best weight: 2.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.8328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 26306 Z= 0.324 Angle : 0.770 13.795 35677 Z= 0.391 Chirality : 0.048 0.246 4180 Planarity : 0.005 0.066 4716 Dihedral : 5.691 32.047 3685 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.59 % Favored : 89.32 % Rotamer: Outliers : 4.55 % Allowed : 22.14 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.20 (0.14), residues: 3399 helix: -0.06 (0.15), residues: 1208 sheet: -1.48 (0.32), residues: 252 loop : -2.50 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 580 HIS 0.016 0.002 HIS C1313 PHE 0.033 0.002 PHE C 156 TYR 0.028 0.002 TYR A 177 ARG 0.019 0.001 ARG D 860 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 312 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8369 (tt) cc_final: 0.7705 (pt) REVERT: A 130 ILE cc_start: 0.6954 (pt) cc_final: 0.6660 (pt) REVERT: B 205 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.7025 (tmm) REVERT: C 24 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7646 (p) REVERT: C 136 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7290 (p90) REVERT: C 138 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7170 (mp) REVERT: C 407 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8320 (mmm160) REVERT: C 629 PHE cc_start: 0.4860 (OUTLIER) cc_final: 0.3849 (t80) REVERT: C 741 MET cc_start: 0.5236 (tpt) cc_final: 0.5025 (tpt) REVERT: C 755 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8649 (tppt) REVERT: C 958 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7872 (tttt) REVERT: C 965 GLN cc_start: 0.8130 (mt0) cc_final: 0.7783 (pt0) REVERT: C 1107 MET cc_start: 0.7639 (mmt) cc_final: 0.7090 (mtp) REVERT: C 1198 LEU cc_start: 0.8044 (tp) cc_final: 0.7427 (tt) REVERT: D 743 MET cc_start: 0.7208 (mmm) cc_final: 0.6726 (mmp) REVERT: D 798 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7216 (mtp85) REVERT: D 1236 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6430 (tt0) REVERT: D 1349 GLU cc_start: 0.6478 (tt0) cc_final: 0.5009 (mp0) REVERT: G 5 MET cc_start: 0.4799 (ppp) cc_final: 0.4339 (ppp) REVERT: G 64 GLU cc_start: 0.6948 (pm20) cc_final: 0.6237 (pm20) REVERT: F 17 MET cc_start: 0.7569 (mmm) cc_final: 0.6025 (ptm) REVERT: F 33 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5559 (pp) REVERT: F 39 MET cc_start: 0.6579 (tpp) cc_final: 0.6200 (tpp) outliers start: 124 outliers final: 97 residues processed: 401 average time/residue: 0.3755 time to fit residues: 240.5698 Evaluate side-chains 413 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 308 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1236 GLU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 311 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.8364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 26306 Z= 0.266 Angle : 0.735 13.863 35677 Z= 0.371 Chirality : 0.047 0.320 4180 Planarity : 0.005 0.080 4716 Dihedral : 5.469 31.555 3685 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.94 % Favored : 90.03 % Rotamer: Outliers : 4.00 % Allowed : 22.84 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.04 (0.14), residues: 3399 helix: 0.16 (0.15), residues: 1200 sheet: -1.39 (0.32), residues: 257 loop : -2.47 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 580 HIS 0.017 0.001 HIS C1313 PHE 0.030 0.002 PHE C 156 TYR 0.029 0.002 TYR A 177 ARG 0.020 0.001 ARG D 860 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 315 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8441 (tt) cc_final: 0.7761 (pt) REVERT: A 130 ILE cc_start: 0.6825 (pt) cc_final: 0.6536 (pt) REVERT: C 135 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7394 (t) REVERT: C 136 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7319 (p90) REVERT: C 138 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7081 (mp) REVERT: C 407 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8318 (mmm160) REVERT: C 629 PHE cc_start: 0.5099 (OUTLIER) cc_final: 0.4162 (t80) REVERT: C 741 MET cc_start: 0.5294 (tpt) cc_final: 0.5031 (tpt) REVERT: C 755 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8631 (tppt) REVERT: C 965 GLN cc_start: 0.8150 (mt0) cc_final: 0.7795 (pt0) REVERT: C 1107 MET cc_start: 0.7657 (mmt) cc_final: 0.6993 (mtp) REVERT: C 1198 LEU cc_start: 0.7928 (tp) cc_final: 0.7599 (tt) REVERT: C 1231 TYR cc_start: 0.7728 (t80) cc_final: 0.7171 (t80) REVERT: C 1314 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: D 130 MET cc_start: 0.5686 (pmm) cc_final: 0.5364 (pmm) REVERT: D 623 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7423 (mp10) REVERT: D 743 MET cc_start: 0.7153 (mmm) cc_final: 0.6654 (mmp) REVERT: D 798 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7123 (mtp85) REVERT: D 1263 LYS cc_start: 0.4633 (tptp) cc_final: 0.3362 (mmtm) REVERT: D 1349 GLU cc_start: 0.6687 (tt0) cc_final: 0.5245 (mp0) REVERT: G 5 MET cc_start: 0.4781 (ppp) cc_final: 0.4366 (ppp) REVERT: G 64 GLU cc_start: 0.7105 (pm20) cc_final: 0.6321 (pm20) REVERT: G 98 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6225 (pp20) REVERT: F 17 MET cc_start: 0.7451 (mmm) cc_final: 0.5939 (ptm) REVERT: F 33 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5622 (pp) outliers start: 109 outliers final: 84 residues processed: 392 average time/residue: 0.3816 time to fit residues: 236.8226 Evaluate side-chains 391 residues out of total 2920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 300 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.0030 chunk 287 optimal weight: 40.0000 chunk 82 optimal weight: 9.9990 chunk 248 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 50.0000 chunk 270 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 277 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.181093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.148899 restraints weight = 43317.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.150263 restraints weight = 60648.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.150899 restraints weight = 49288.378| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.8378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26306 Z= 0.222 Angle : 0.708 13.704 35677 Z= 0.357 Chirality : 0.046 0.360 4180 Planarity : 0.004 0.052 4716 Dihedral : 5.279 30.628 3685 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.33 % Favored : 90.64 % Rotamer: Outliers : 3.34 % Allowed : 23.57 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -1.88 (0.14), residues: 3399 helix: 0.33 (0.15), residues: 1196 sheet: -1.31 (0.32), residues: 257 loop : -2.40 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D1193 HIS 0.008 0.001 HIS C1313 PHE 0.041 0.002 PHE C 195 TYR 0.029 0.002 TYR D 382 ARG 0.011 0.001 ARG C1033 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5846.91 seconds wall clock time: 106 minutes 52.23 seconds (6412.23 seconds total)