Starting phenix.real_space_refine on Sat Feb 17 12:20:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/02_2024/7jpw_22425_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/02_2024/7jpw_22425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/02_2024/7jpw_22425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/02_2024/7jpw_22425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/02_2024/7jpw_22425_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpw_22425/02_2024/7jpw_22425_updated.pdb" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 10 5.49 5 S 109 5.16 5 C 12126 2.51 5 N 2985 2.21 5 O 3349 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 598": "OD1" <-> "OD2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1196": "OD1" <-> "OD2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A PHE 1260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1343": "OD1" <-> "OD2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A TYR 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A GLU 1408": "OE1" <-> "OE2" Residue "A GLU 1412": "OE1" <-> "OE2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 373": "OE1" <-> "OE2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F GLU 476": "OE1" <-> "OE2" Residue "F ASP 493": "OD1" <-> "OD2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 603": "OD1" <-> "OD2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F ASP 654": "OD1" <-> "OD2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 668": "OD1" <-> "OD2" Residue "F ASP 677": "OD1" <-> "OD2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F ASP 711": "OD1" <-> "OD2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F GLU 753": "OE1" <-> "OE2" Residue "F TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 774": "OD1" <-> "OD2" Residue "F TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ASP 849": "OD1" <-> "OD2" Residue "F ASP 869": "OD1" <-> "OD2" Residue "F GLU 880": "OE1" <-> "OE2" Residue "F ASP 882": "OD1" <-> "OD2" Residue "F PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 987": "OD1" <-> "OD2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F GLU 1069": "OE1" <-> "OE2" Residue "F ASP 1070": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18583 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 9009 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1078} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 444 Unusual residues: {' CA': 1, '3PE': 9, 'PC1': 1, 'VFY': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 13.11, per 1000 atoms: 0.71 Number of scatterers: 18583 At special positions: 0 Unit cell: (144.82, 137.022, 158.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 109 16.00 P 10 15.00 F 3 9.00 O 3349 8.00 N 2985 7.00 C 12126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.02 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.04 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.17 Conformation dependent library (CDL) restraints added in 4.4 seconds 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 12 sheets defined 47.2% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 53 through 69 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.617A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.535A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.678A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 3.708A pdb=" N SER A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 195 through 217 removed outlier: 4.201A pdb=" N HIS A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 199 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 205 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 207 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 211 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.092A pdb=" N VAL A 315 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR A 316 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 318 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 319 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 344 removed outlier: 3.879A pdb=" N LYS A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 451 removed outlier: 4.266A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 485 removed outlier: 4.057A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.712A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 527 through 540 removed outlier: 4.063A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 549 through 558 removed outlier: 4.495A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.626A pdb=" N LEU A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 632 through 646 removed outlier: 3.996A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N CYS A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.666A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 671 Processing helix chain 'A' and resid 802 through 817 removed outlier: 4.250A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 812 " --> pdb=" O PHE A 808 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 844 removed outlier: 4.036A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 851 No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 869 through 881 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.511A pdb=" N VAL A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 915 through 923 removed outlier: 3.523A pdb=" N CYS A 920 " --> pdb=" O HIS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 950 removed outlier: 3.614A pdb=" N LEU A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1039 through 1051 removed outlier: 3.775A pdb=" N ALA A1042 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A1044 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A1047 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A1048 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A1049 " --> pdb=" O ILE A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1068 removed outlier: 4.051A pdb=" N VAL A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 4.268A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 removed outlier: 4.283A pdb=" N ALA A1126 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1172 removed outlier: 3.944A pdb=" N ALA A1171 " --> pdb=" O LEU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1205 removed outlier: 3.635A pdb=" N ILE A1191 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1192 " --> pdb=" O LEU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1248 removed outlier: 3.818A pdb=" N ARG A1239 " --> pdb=" O ARG A1236 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A1242 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A1248 " --> pdb=" O LYS A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1264 removed outlier: 3.798A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1288 removed outlier: 3.519A pdb=" N LEU A1273 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1331 Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 4.299A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A1365 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A1371 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A1372 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A1378 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A1382 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A1387 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 removed outlier: 3.582A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1427 No H-bonds generated for 'chain 'A' and resid 1425 through 1427' Processing helix chain 'E' and resid 7 through 25 Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 135 through 163 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 181 through 203 Processing helix chain 'F' and resid 30 through 52 Processing helix chain 'F' and resid 54 through 64 removed outlier: 4.058A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 110 removed outlier: 3.734A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.545A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 284 removed outlier: 4.155A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.804A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 removed outlier: 3.786A pdb=" N LEU F 347 " --> pdb=" O PHE F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 419 through 425 removed outlier: 4.824A pdb=" N ILE F 423 " --> pdb=" O GLY F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 434 through 439 Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'F' and resid 496 through 499 No H-bonds generated for 'chain 'F' and resid 496 through 499' Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 641 through 650 removed outlier: 3.714A pdb=" N THR F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 5.489A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 702 through 721 Processing helix chain 'F' and resid 723 through 725 No H-bonds generated for 'chain 'F' and resid 723 through 725' Processing helix chain 'F' and resid 749 through 753 removed outlier: 3.659A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 763 No H-bonds generated for 'chain 'F' and resid 761 through 763' Processing helix chain 'F' and resid 765 through 772 removed outlier: 3.512A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 829 Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 892 Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= C, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= D, first strand: chain 'E' and resid 48 through 50 Processing sheet with id= E, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= F, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.903A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 300 through 302 removed outlier: 8.007A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR F 411 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER F 390 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR F 413 " --> pdb=" O SER F 390 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= I, first strand: chain 'F' and resid 662 through 664 removed outlier: 4.089A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 992 through 997 removed outlier: 6.001A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP F 857 " --> pdb=" O LEU F 862 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 862 " --> pdb=" O ASP F 857 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 895 through 902 removed outlier: 4.341A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 905 through 907 732 hydrogen bonds defined for protein. 1898 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: 6.18 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2981 1.31 - 1.45: 5361 1.45 - 1.58: 10467 1.58 - 1.72: 20 1.72 - 1.86: 168 Bond restraints: 18997 Sorted by residual: bond pdb=" C05 VFY A1912 " pdb=" C06 VFY A1912 " ideal model delta sigma weight residual 1.375 1.532 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C09 VFY A1912 " pdb=" C11 VFY A1912 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C21 3PE A1907 " pdb=" O21 3PE A1907 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 18992 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.82: 315 104.82 - 112.16: 9401 112.16 - 119.51: 6567 119.51 - 126.86: 9182 126.86 - 134.20: 214 Bond angle restraints: 25679 Sorted by residual: angle pdb=" C SER E 81 " pdb=" N TYR E 82 " pdb=" CA TYR E 82 " ideal model delta sigma weight residual 121.29 132.21 -10.92 1.74e+00 3.30e-01 3.94e+01 angle pdb=" N VAL A 661 " pdb=" CA VAL A 661 " pdb=" C VAL A 661 " ideal model delta sigma weight residual 113.71 107.85 5.86 9.50e-01 1.11e+00 3.80e+01 angle pdb=" C TYR A 541 " pdb=" N TRP A 542 " pdb=" CA TRP A 542 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" N LEU A 522 " pdb=" CA LEU A 522 " pdb=" C LEU A 522 " ideal model delta sigma weight residual 111.36 105.62 5.74 1.09e+00 8.42e-01 2.77e+01 angle pdb=" N PHE A 536 " pdb=" CA PHE A 536 " pdb=" C PHE A 536 " ideal model delta sigma weight residual 111.28 116.17 -4.89 1.09e+00 8.42e-01 2.01e+01 ... (remaining 25674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 9520 17.76 - 35.53: 1304 35.53 - 53.29: 473 53.29 - 71.06: 118 71.06 - 88.82: 29 Dihedral angle restraints: 11444 sinusoidal: 4828 harmonic: 6616 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -146.18 60.18 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA ASP F 227 " pdb=" C ASP F 227 " pdb=" N ASN F 228 " pdb=" CA ASN F 228 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP F 518 " pdb=" C ASP F 518 " pdb=" N PRO F 519 " pdb=" CA PRO F 519 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1936 0.056 - 0.112: 765 0.112 - 0.168: 127 0.168 - 0.224: 18 0.224 - 0.281: 2 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA TRP A 542 " pdb=" N TRP A 542 " pdb=" C TRP A 542 " pdb=" CB TRP A 542 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" C PRO A 268 " pdb=" CB PRO A 268 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN F 379 " pdb=" N ASN F 379 " pdb=" C ASN F 379 " pdb=" CB ASN F 379 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2845 not shown) Planarity restraints: 3203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 81 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C SER E 81 " -0.051 2.00e-02 2.50e+03 pdb=" O SER E 81 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR E 82 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 75 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 52 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.034 5.00e-02 4.00e+02 ... (remaining 3200 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 373 2.63 - 3.20: 17255 3.20 - 3.77: 27385 3.77 - 4.33: 39899 4.33 - 4.90: 65794 Nonbonded interactions: 150706 Sorted by model distance: nonbonded pdb=" OD2 ASP F 711 " pdb=" OG1 THR F 739 " model vdw 2.068 2.440 nonbonded pdb=" N 3PE A1906 " pdb=" O11 3PE A1906 " model vdw 2.079 2.520 nonbonded pdb=" N 3PE A1911 " pdb=" O14 3PE A1911 " model vdw 2.079 2.520 nonbonded pdb=" O SER A1232 " pdb=" OG SER A1232 " model vdw 2.105 2.440 nonbonded pdb=" OH TYR F 452 " pdb=" OG1 THR F 463 " model vdw 2.121 2.440 ... (remaining 150701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.010 Extract box with map and model: 5.890 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 54.620 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.015 0.157 18997 Z= 0.962 Angle : 1.060 11.014 25679 Z= 0.555 Chirality : 0.058 0.281 2848 Planarity : 0.006 0.062 3203 Dihedral : 19.261 88.820 7133 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.64 % Favored : 90.27 % Rotamer: Outliers : 11.04 % Allowed : 20.28 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -4.54 (0.14), residues: 2222 helix: -2.69 (0.12), residues: 1094 sheet: -2.28 (0.30), residues: 219 loop : -3.51 (0.16), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A1016 HIS 0.007 0.001 HIS A 453 PHE 0.027 0.003 PHE F 157 TYR 0.023 0.003 TYR A1334 ARG 0.007 0.001 ARG F 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 208 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.5991 (pt0) REVERT: A 100 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5909 (tp30) REVERT: A 447 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8111 (tp) REVERT: A 449 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8574 (mt) REVERT: A 510 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5313 (tm-30) REVERT: A 565 LEU cc_start: 0.9131 (tt) cc_final: 0.8913 (tp) REVERT: A 666 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.5297 (mp0) REVERT: A 936 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8423 (m) REVERT: A 984 GLU cc_start: 0.7498 (tt0) cc_final: 0.7223 (tt0) REVERT: A 1036 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8668 (m-40) REVERT: A 1096 ARG cc_start: 0.6379 (mtp180) cc_final: 0.6142 (mtt-85) REVERT: A 1383 ASN cc_start: 0.7939 (m110) cc_final: 0.7736 (m110) REVERT: A 1427 ARG cc_start: 0.4105 (OUTLIER) cc_final: 0.2343 (mpp80) REVERT: E 5 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: E 59 LYS cc_start: 0.2835 (OUTLIER) cc_final: 0.1760 (mtpt) REVERT: E 130 ARG cc_start: 0.6490 (ttp-110) cc_final: 0.5832 (mtm110) REVERT: E 133 ARG cc_start: 0.3090 (mmt180) cc_final: 0.2885 (mmt180) REVERT: E 164 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.3609 (ppt170) REVERT: F 88 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8840 (ttmm) REVERT: F 158 ARG cc_start: 0.8002 (mpp80) cc_final: 0.7546 (mtm-85) REVERT: F 256 MET cc_start: 0.9068 (ttm) cc_final: 0.8868 (ttm) REVERT: F 330 LYS cc_start: 0.8538 (tttm) cc_final: 0.8255 (ttmt) REVERT: F 442 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8736 (mtpp) REVERT: F 908 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6119 (mm-30) REVERT: F 1020 MET cc_start: 0.7930 (ttp) cc_final: 0.7680 (ttp) outliers start: 220 outliers final: 156 residues processed: 408 average time/residue: 0.2870 time to fit residues: 180.6113 Evaluate side-chains 358 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 187 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 505 CYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1100 CYS Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1342 SER Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 442 LYS Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 596 SER Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 672 ASP Chi-restraints excluded: chain F residue 678 ASN Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 770 SER Chi-restraints excluded: chain F residue 775 ASN Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 881 ILE Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 908 GLU Chi-restraints excluded: chain F residue 976 SER Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 239 ASN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 453 HIS A 803 ASN A 909 ASN A 958 ASN A 999 ASN A1058 ASN A1138 GLN A1154 ASN A1183 ASN A1383 ASN A1398 HIS E 209 GLN F 56 GLN F 164 GLN F 169 HIS F 308 HIS F 470 ASN F 511 ASN F 551 GLN F 556 GLN F 644 GLN F 679 ASN F 685 ASN F 720 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 888 HIS F 988 ASN F1039 GLN F1065 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18997 Z= 0.181 Angle : 0.578 8.462 25679 Z= 0.296 Chirality : 0.041 0.172 2848 Planarity : 0.005 0.054 3203 Dihedral : 15.088 85.692 3164 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.57 % Allowed : 23.34 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.84 (0.16), residues: 2222 helix: -1.17 (0.15), residues: 1101 sheet: -1.90 (0.31), residues: 220 loop : -2.71 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 187 HIS 0.004 0.001 HIS A 453 PHE 0.016 0.001 PHE F 515 TYR 0.025 0.001 TYR F 629 ARG 0.002 0.000 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 229 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 53 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: A 54 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5828 (pp20) REVERT: A 74 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8049 (mtm) REVERT: A 100 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6159 (tp30) REVERT: A 201 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8765 (tp) REVERT: A 262 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7438 (ttm170) REVERT: A 341 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7742 (ttp80) REVERT: A 479 MET cc_start: 0.4580 (ppp) cc_final: 0.4192 (ppp) REVERT: A 510 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6007 (tm-30) REVERT: A 666 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5230 (mp0) REVERT: A 919 GLN cc_start: 0.4710 (OUTLIER) cc_final: 0.3842 (mm-40) REVERT: A 958 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8220 (m110) REVERT: A 984 GLU cc_start: 0.7489 (tt0) cc_final: 0.7179 (tt0) REVERT: A 1096 ARG cc_start: 0.6352 (mtp180) cc_final: 0.6142 (mtt-85) REVERT: A 1121 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7004 (tm-30) REVERT: A 1165 MET cc_start: 0.8428 (tmm) cc_final: 0.8028 (tmm) REVERT: A 1186 ASP cc_start: 0.8012 (m-30) cc_final: 0.7755 (m-30) REVERT: A 1421 ASP cc_start: 0.2306 (OUTLIER) cc_final: 0.1415 (t70) REVERT: E 31 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.6204 (t-90) REVERT: E 130 ARG cc_start: 0.6425 (ttp-110) cc_final: 0.5823 (mtm110) REVERT: E 133 ARG cc_start: 0.3058 (mmt180) cc_final: 0.2722 (mmt180) REVERT: F 230 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5809 (tpt170) REVERT: F 330 LYS cc_start: 0.8502 (tttm) cc_final: 0.8161 (ttmt) REVERT: F 817 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8667 (tt) REVERT: F 1020 MET cc_start: 0.7906 (ttp) cc_final: 0.7553 (ttp) outliers start: 111 outliers final: 63 residues processed: 325 average time/residue: 0.2964 time to fit residues: 147.8817 Evaluate side-chains 280 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1342 SER Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 672 ASP Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 203 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 69 optimal weight: 0.0970 chunk 163 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 ASN E 209 GLN F 644 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18997 Z= 0.181 Angle : 0.546 7.981 25679 Z= 0.278 Chirality : 0.041 0.152 2848 Planarity : 0.004 0.052 3203 Dihedral : 13.279 85.658 2968 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.82 % Allowed : 23.64 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.19 (0.17), residues: 2222 helix: -0.63 (0.15), residues: 1117 sheet: -1.68 (0.32), residues: 220 loop : -2.40 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.003 0.001 HIS A 274 PHE 0.014 0.001 PHE F 515 TYR 0.023 0.001 TYR F 629 ARG 0.004 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 223 time to evaluate : 2.028 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.5681 (mp0) REVERT: A 74 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8598 (mtm) REVERT: A 100 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6147 (tp30) REVERT: A 108 TYR cc_start: 0.7041 (m-80) cc_final: 0.6771 (m-80) REVERT: A 113 HIS cc_start: 0.4870 (p-80) cc_final: 0.4484 (p-80) REVERT: A 201 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8755 (tp) REVERT: A 341 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7768 (ttp80) REVERT: A 479 MET cc_start: 0.4485 (ppp) cc_final: 0.4227 (ppp) REVERT: A 484 TYR cc_start: 0.5421 (OUTLIER) cc_final: 0.4271 (t80) REVERT: A 510 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6345 (tm-30) REVERT: A 666 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5290 (mp0) REVERT: A 919 GLN cc_start: 0.4632 (OUTLIER) cc_final: 0.3915 (mm110) REVERT: A 958 ASN cc_start: 0.8501 (m-40) cc_final: 0.8273 (m110) REVERT: A 984 GLU cc_start: 0.7504 (tt0) cc_final: 0.7199 (tt0) REVERT: A 1063 PHE cc_start: 0.7334 (t80) cc_final: 0.6836 (t80) REVERT: A 1121 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 1165 MET cc_start: 0.8451 (tmm) cc_final: 0.8109 (tmm) REVERT: A 1421 ASP cc_start: 0.2088 (OUTLIER) cc_final: 0.1332 (t70) REVERT: E 10 ARG cc_start: 0.6509 (mtp180) cc_final: 0.6188 (mmm160) REVERT: E 31 HIS cc_start: 0.6609 (m-70) cc_final: 0.6186 (t-90) REVERT: E 120 MET cc_start: 0.7703 (mmt) cc_final: 0.7391 (mmm) REVERT: E 130 ARG cc_start: 0.6451 (ttp-110) cc_final: 0.5834 (mtm110) REVERT: E 133 ARG cc_start: 0.3007 (mmt180) cc_final: 0.2682 (mmt180) REVERT: E 191 LEU cc_start: 0.8628 (mt) cc_final: 0.8064 (tp) REVERT: E 216 MET cc_start: 0.6516 (tmm) cc_final: 0.6252 (tmm) REVERT: F 230 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5738 (tpt170) REVERT: F 330 LYS cc_start: 0.8511 (tttm) cc_final: 0.8198 (ttmt) REVERT: F 817 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8661 (tt) outliers start: 96 outliers final: 68 residues processed: 302 average time/residue: 0.3284 time to fit residues: 155.1301 Evaluate side-chains 284 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 206 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1421 ASP Chi-restraints excluded: chain A residue 1423 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN A1287 GLN F 165 HIS F 655 ASN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18997 Z= 0.167 Angle : 0.519 7.792 25679 Z= 0.265 Chirality : 0.040 0.142 2848 Planarity : 0.004 0.051 3203 Dihedral : 12.326 87.888 2948 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.57 % Allowed : 24.65 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2222 helix: -0.29 (0.16), residues: 1118 sheet: -1.48 (0.32), residues: 220 loop : -2.13 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 187 HIS 0.003 0.000 HIS A 274 PHE 0.023 0.001 PHE F 689 TYR 0.020 0.001 TYR F 629 ARG 0.002 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 216 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.5570 (mp0) REVERT: A 51 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.5110 (ttpp) REVERT: A 53 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: A 54 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6348 (pp20) REVERT: A 74 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8576 (mtm) REVERT: A 90 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6692 (mm-30) REVERT: A 100 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6207 (tp30) REVERT: A 201 LEU cc_start: 0.9097 (tt) cc_final: 0.8778 (tp) REVERT: A 341 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7792 (ttp80) REVERT: A 479 MET cc_start: 0.4588 (ppp) cc_final: 0.4366 (ppp) REVERT: A 484 TYR cc_start: 0.5416 (OUTLIER) cc_final: 0.4273 (t80) REVERT: A 510 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6010 (tm-30) REVERT: A 666 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5176 (mp0) REVERT: A 919 GLN cc_start: 0.4560 (OUTLIER) cc_final: 0.3943 (mm110) REVERT: A 958 ASN cc_start: 0.8472 (m-40) cc_final: 0.8115 (m-40) REVERT: A 984 GLU cc_start: 0.7569 (tt0) cc_final: 0.7244 (tt0) REVERT: A 1054 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7096 (m-10) REVERT: A 1063 PHE cc_start: 0.7367 (t80) cc_final: 0.6993 (t80) REVERT: A 1094 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6535 (mmtt) REVERT: A 1165 MET cc_start: 0.8431 (tmm) cc_final: 0.8063 (tmm) REVERT: A 1244 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 1412 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6525 (mm-30) REVERT: A 1426 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.4110 (mp) REVERT: E 10 ARG cc_start: 0.6559 (mtp180) cc_final: 0.6218 (mmm160) REVERT: E 130 ARG cc_start: 0.6471 (ttp-110) cc_final: 0.5776 (mtm110) REVERT: E 191 LEU cc_start: 0.8666 (mt) cc_final: 0.8203 (tp) REVERT: E 216 MET cc_start: 0.6551 (tmm) cc_final: 0.6231 (tmm) REVERT: F 230 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.5567 (tpt170) REVERT: F 330 LYS cc_start: 0.8512 (tttm) cc_final: 0.8172 (ttmt) REVERT: F 817 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8655 (tt) REVERT: F 997 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8304 (pp) REVERT: F 1020 MET cc_start: 0.7866 (ttp) cc_final: 0.7492 (ttp) outliers start: 91 outliers final: 53 residues processed: 292 average time/residue: 0.3076 time to fit residues: 139.1440 Evaluate side-chains 273 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 203 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1094 LYS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 chunk 3 optimal weight: 0.0030 chunk 161 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 1.7472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A1058 ASN F 644 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18997 Z= 0.250 Angle : 0.555 9.934 25679 Z= 0.281 Chirality : 0.042 0.157 2848 Planarity : 0.004 0.051 3203 Dihedral : 11.942 85.801 2916 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.07 % Allowed : 24.20 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2222 helix: -0.23 (0.15), residues: 1123 sheet: -1.37 (0.32), residues: 220 loop : -2.06 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1016 HIS 0.008 0.001 HIS A 113 PHE 0.016 0.001 PHE F 157 TYR 0.016 0.001 TYR F 629 ARG 0.002 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 209 time to evaluate : 2.361 Fit side-chains REVERT: A 49 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: A 51 LYS cc_start: 0.5412 (OUTLIER) cc_final: 0.5181 (ttpp) REVERT: A 53 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: A 54 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6307 (pp20) REVERT: A 74 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8593 (mtm) REVERT: A 90 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6676 (mm-30) REVERT: A 100 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6196 (tp30) REVERT: A 201 LEU cc_start: 0.9105 (tt) cc_final: 0.8761 (tp) REVERT: A 484 TYR cc_start: 0.5441 (OUTLIER) cc_final: 0.4297 (t80) REVERT: A 510 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: A 666 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5421 (mp0) REVERT: A 919 GLN cc_start: 0.4589 (OUTLIER) cc_final: 0.3967 (mm110) REVERT: A 984 GLU cc_start: 0.7516 (tt0) cc_final: 0.7186 (tt0) REVERT: A 1054 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: A 1063 PHE cc_start: 0.7351 (t80) cc_final: 0.6945 (t80) REVERT: A 1094 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6407 (mmtt) REVERT: A 1121 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6771 (tm-30) REVERT: A 1165 MET cc_start: 0.8457 (tmm) cc_final: 0.8034 (tmm) REVERT: A 1412 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6505 (mm-30) REVERT: A 1426 LEU cc_start: 0.4341 (OUTLIER) cc_final: 0.4139 (mp) REVERT: E 10 ARG cc_start: 0.6602 (mtp180) cc_final: 0.6220 (mmm160) REVERT: E 120 MET cc_start: 0.7756 (mmt) cc_final: 0.7460 (mmm) REVERT: E 130 ARG cc_start: 0.6393 (ttp-110) cc_final: 0.5863 (mtm110) REVERT: F 59 ASP cc_start: 0.7605 (t0) cc_final: 0.7306 (t0) REVERT: F 230 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5689 (tpt170) REVERT: F 330 LYS cc_start: 0.8546 (tttm) cc_final: 0.8223 (ttmt) REVERT: F 817 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8691 (tt) REVERT: F 1020 MET cc_start: 0.7917 (ttp) cc_final: 0.7560 (ttp) outliers start: 101 outliers final: 68 residues processed: 297 average time/residue: 0.3132 time to fit residues: 146.8041 Evaluate side-chains 282 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 199 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1094 LYS Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 100 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 ASN E 209 GLN F 484 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18997 Z= 0.135 Angle : 0.507 14.099 25679 Z= 0.255 Chirality : 0.039 0.140 2848 Planarity : 0.004 0.050 3203 Dihedral : 11.397 86.437 2916 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.87 % Allowed : 24.70 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2222 helix: 0.14 (0.16), residues: 1107 sheet: -1.22 (0.32), residues: 220 loop : -1.92 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.006 0.001 HIS A 113 PHE 0.024 0.001 PHE F 689 TYR 0.017 0.001 TYR F 629 ARG 0.002 0.000 ARG F1032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 221 time to evaluate : 2.090 Fit side-chains revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.5586 (mp0) REVERT: A 51 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5279 (ttpp) REVERT: A 53 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: A 54 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5942 (pp20) REVERT: A 74 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: A 90 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6752 (mm-30) REVERT: A 100 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6223 (tp30) REVERT: A 201 LEU cc_start: 0.9059 (tt) cc_final: 0.8829 (tp) REVERT: A 484 TYR cc_start: 0.5491 (OUTLIER) cc_final: 0.4335 (t80) REVERT: A 666 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5114 (mp0) REVERT: A 900 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7136 (ptt90) REVERT: A 919 GLN cc_start: 0.4331 (OUTLIER) cc_final: 0.3851 (mm110) REVERT: A 958 ASN cc_start: 0.8347 (m-40) cc_final: 0.8082 (m-40) REVERT: A 984 GLU cc_start: 0.7554 (tt0) cc_final: 0.7216 (tt0) REVERT: A 1054 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7091 (m-10) REVERT: A 1063 PHE cc_start: 0.7279 (t80) cc_final: 0.6831 (t80) REVERT: A 1094 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6306 (mmtt) REVERT: A 1116 THR cc_start: 0.7068 (m) cc_final: 0.6796 (m) REVERT: A 1121 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7031 (tm-30) REVERT: A 1165 MET cc_start: 0.8455 (tmm) cc_final: 0.8047 (tmm) REVERT: A 1412 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: E 10 ARG cc_start: 0.6613 (mtp180) cc_final: 0.6227 (mmm160) REVERT: E 50 HIS cc_start: 0.5940 (m-70) cc_final: 0.5488 (m-70) REVERT: E 120 MET cc_start: 0.7747 (mmt) cc_final: 0.7451 (mmm) REVERT: E 130 ARG cc_start: 0.6312 (ttp-110) cc_final: 0.5857 (mtm110) REVERT: E 137 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8428 (mt) REVERT: E 191 LEU cc_start: 0.8537 (mt) cc_final: 0.7856 (tp) REVERT: E 216 MET cc_start: 0.6371 (tmm) cc_final: 0.6033 (tmm) REVERT: F 59 ASP cc_start: 0.7567 (t0) cc_final: 0.7279 (t0) REVERT: F 230 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5857 (tpt170) REVERT: F 330 LYS cc_start: 0.8455 (tttm) cc_final: 0.8093 (ttmt) REVERT: F 817 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8614 (tt) REVERT: F 858 ASP cc_start: 0.8398 (p0) cc_final: 0.7945 (p0) REVERT: F 1020 MET cc_start: 0.7894 (ttp) cc_final: 0.7536 (ttp) outliers start: 97 outliers final: 62 residues processed: 304 average time/residue: 0.2805 time to fit residues: 133.5089 Evaluate side-chains 282 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 205 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1094 LYS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN E 209 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18997 Z= 0.187 Angle : 0.531 12.129 25679 Z= 0.266 Chirality : 0.040 0.141 2848 Planarity : 0.004 0.050 3203 Dihedral : 11.175 89.386 2906 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.72 % Allowed : 24.70 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2222 helix: 0.19 (0.16), residues: 1116 sheet: -1.10 (0.33), residues: 220 loop : -1.86 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 122 HIS 0.006 0.001 HIS A 113 PHE 0.022 0.001 PHE F 689 TYR 0.010 0.001 TYR F 629 ARG 0.002 0.000 ARG A1249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 213 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.5845 (mp0) REVERT: A 51 LYS cc_start: 0.5581 (OUTLIER) cc_final: 0.5292 (ttpp) REVERT: A 53 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: A 54 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6130 (pp20) REVERT: A 62 PHE cc_start: 0.8357 (t80) cc_final: 0.8112 (t80) REVERT: A 74 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8539 (mtm) REVERT: A 90 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6751 (mm-30) REVERT: A 100 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6281 (tp30) REVERT: A 201 LEU cc_start: 0.9062 (tt) cc_final: 0.8829 (tp) REVERT: A 484 TYR cc_start: 0.5278 (OUTLIER) cc_final: 0.4155 (t80) REVERT: A 531 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6574 (mtt90) REVERT: A 666 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.5127 (mp0) REVERT: A 900 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7135 (ptt90) REVERT: A 919 GLN cc_start: 0.4314 (OUTLIER) cc_final: 0.3834 (mm110) REVERT: A 958 ASN cc_start: 0.8390 (m-40) cc_final: 0.8132 (m-40) REVERT: A 984 GLU cc_start: 0.7540 (tt0) cc_final: 0.7205 (tt0) REVERT: A 1054 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7114 (m-10) REVERT: A 1063 PHE cc_start: 0.7310 (t80) cc_final: 0.6869 (t80) REVERT: A 1094 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6272 (mmtt) REVERT: A 1116 THR cc_start: 0.7113 (m) cc_final: 0.6871 (m) REVERT: A 1121 GLU cc_start: 0.7509 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 1165 MET cc_start: 0.8504 (tmm) cc_final: 0.8077 (tmm) REVERT: A 1412 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6494 (mm-30) REVERT: E 10 ARG cc_start: 0.6593 (mtp180) cc_final: 0.6201 (mmm160) REVERT: E 50 HIS cc_start: 0.5949 (m-70) cc_final: 0.5542 (m-70) REVERT: E 120 MET cc_start: 0.7772 (mmt) cc_final: 0.7470 (mmm) REVERT: E 130 ARG cc_start: 0.6178 (ttp-110) cc_final: 0.5842 (mtm110) REVERT: E 137 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8387 (mt) REVERT: E 191 LEU cc_start: 0.8630 (mt) cc_final: 0.7937 (tp) REVERT: F 59 ASP cc_start: 0.7544 (t0) cc_final: 0.7243 (t0) REVERT: F 205 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8804 (tt) REVERT: F 230 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5901 (tpt170) REVERT: F 330 LYS cc_start: 0.8487 (tttm) cc_final: 0.8167 (ttmt) REVERT: F 817 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8667 (tt) REVERT: F 858 ASP cc_start: 0.8406 (p0) cc_final: 0.7941 (p0) REVERT: F 1020 MET cc_start: 0.7921 (ttp) cc_final: 0.7559 (ttp) outliers start: 94 outliers final: 66 residues processed: 292 average time/residue: 0.2890 time to fit residues: 131.5850 Evaluate side-chains 293 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 210 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1094 LYS Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN E 209 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18997 Z= 0.156 Angle : 0.518 13.272 25679 Z= 0.258 Chirality : 0.040 0.136 2848 Planarity : 0.004 0.050 3203 Dihedral : 10.899 83.650 2906 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.42 % Allowed : 25.30 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2222 helix: 0.41 (0.16), residues: 1098 sheet: -1.05 (0.33), residues: 220 loop : -1.80 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 187 HIS 0.006 0.001 HIS A 113 PHE 0.025 0.001 PHE F 689 TYR 0.011 0.001 TYR A 108 ARG 0.002 0.000 ARG A1249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 215 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.5743 (mp0) REVERT: A 51 LYS cc_start: 0.5521 (OUTLIER) cc_final: 0.5262 (ttpp) REVERT: A 53 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: A 54 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6059 (pp20) REVERT: A 62 PHE cc_start: 0.8363 (t80) cc_final: 0.8127 (t80) REVERT: A 74 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8514 (mtm) REVERT: A 76 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 90 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 100 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6197 (tp30) REVERT: A 201 LEU cc_start: 0.9065 (tt) cc_final: 0.8823 (tp) REVERT: A 484 TYR cc_start: 0.5270 (OUTLIER) cc_final: 0.4021 (t80) REVERT: A 900 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7141 (ptt90) REVERT: A 958 ASN cc_start: 0.8372 (m-40) cc_final: 0.8110 (m-40) REVERT: A 984 GLU cc_start: 0.7512 (tt0) cc_final: 0.7171 (tt0) REVERT: A 1031 MET cc_start: 0.8774 (mtp) cc_final: 0.8378 (mtp) REVERT: A 1063 PHE cc_start: 0.7256 (t80) cc_final: 0.6863 (t80) REVERT: A 1116 THR cc_start: 0.7038 (m) cc_final: 0.6829 (m) REVERT: A 1121 GLU cc_start: 0.7529 (tm-30) cc_final: 0.6737 (tm-30) REVERT: A 1165 MET cc_start: 0.8512 (tmm) cc_final: 0.8082 (tmm) REVERT: A 1412 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: E 50 HIS cc_start: 0.5974 (m-70) cc_final: 0.5596 (m-70) REVERT: E 120 MET cc_start: 0.7745 (mmt) cc_final: 0.7470 (mmm) REVERT: E 130 ARG cc_start: 0.6063 (ttp-110) cc_final: 0.5790 (mtm110) REVERT: E 137 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8335 (mt) REVERT: E 191 LEU cc_start: 0.8638 (mt) cc_final: 0.7988 (tp) REVERT: F 59 ASP cc_start: 0.7596 (t0) cc_final: 0.7275 (t0) REVERT: F 230 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5843 (tpt170) REVERT: F 330 LYS cc_start: 0.8469 (tttm) cc_final: 0.8144 (ttmt) REVERT: F 858 ASP cc_start: 0.8380 (p0) cc_final: 0.7901 (p0) REVERT: F 1002 CYS cc_start: 0.5214 (OUTLIER) cc_final: 0.3956 (p) REVERT: F 1020 MET cc_start: 0.7885 (ttp) cc_final: 0.7509 (ttp) outliers start: 88 outliers final: 63 residues processed: 289 average time/residue: 0.2939 time to fit residues: 133.8374 Evaluate side-chains 286 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 212 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 230 ARG Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN E 209 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18997 Z= 0.156 Angle : 0.523 10.507 25679 Z= 0.259 Chirality : 0.040 0.136 2848 Planarity : 0.004 0.050 3203 Dihedral : 10.610 81.545 2898 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.87 % Allowed : 25.35 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2222 helix: 0.53 (0.16), residues: 1098 sheet: -0.98 (0.33), residues: 220 loop : -1.73 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 122 HIS 0.007 0.001 HIS A 113 PHE 0.024 0.001 PHE F 689 TYR 0.012 0.001 TYR A 108 ARG 0.004 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 221 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.5871 (mp0) REVERT: A 51 LYS cc_start: 0.5465 (OUTLIER) cc_final: 0.5212 (ttpp) REVERT: A 53 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: A 54 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6049 (pp20) REVERT: A 62 PHE cc_start: 0.8357 (t80) cc_final: 0.8121 (t80) REVERT: A 74 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8497 (mtm) REVERT: A 76 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 90 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6812 (mm-30) REVERT: A 100 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6068 (tp30) REVERT: A 201 LEU cc_start: 0.9064 (tt) cc_final: 0.8818 (tp) REVERT: A 484 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.4060 (t80) REVERT: A 666 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5047 (mp0) REVERT: A 900 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7033 (ptt90) REVERT: A 958 ASN cc_start: 0.8377 (m-40) cc_final: 0.8104 (m-40) REVERT: A 984 GLU cc_start: 0.7504 (tt0) cc_final: 0.7151 (tt0) REVERT: A 1031 MET cc_start: 0.8756 (mtp) cc_final: 0.8361 (mtp) REVERT: A 1063 PHE cc_start: 0.7219 (t80) cc_final: 0.6886 (t80) REVERT: A 1121 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 1165 MET cc_start: 0.8511 (tmm) cc_final: 0.8079 (tmm) REVERT: A 1412 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: E 10 ARG cc_start: 0.6574 (mtp180) cc_final: 0.6203 (mmm160) REVERT: E 50 HIS cc_start: 0.5960 (m-70) cc_final: 0.5641 (m-70) REVERT: E 120 MET cc_start: 0.7740 (mmt) cc_final: 0.7471 (mmm) REVERT: E 130 ARG cc_start: 0.5963 (ttp-110) cc_final: 0.5579 (mtm110) REVERT: E 137 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8283 (mt) REVERT: E 191 LEU cc_start: 0.8603 (mt) cc_final: 0.7971 (tp) REVERT: E 216 MET cc_start: 0.6074 (tmm) cc_final: 0.5793 (tmm) REVERT: F 59 ASP cc_start: 0.7594 (t0) cc_final: 0.7274 (t0) REVERT: F 330 LYS cc_start: 0.8479 (tttm) cc_final: 0.8153 (ttmt) REVERT: F 858 ASP cc_start: 0.8337 (p0) cc_final: 0.7863 (p0) REVERT: F 1002 CYS cc_start: 0.5154 (OUTLIER) cc_final: 0.3928 (p) REVERT: F 1020 MET cc_start: 0.7916 (ttp) cc_final: 0.7576 (ttp) outliers start: 77 outliers final: 58 residues processed: 284 average time/residue: 0.2889 time to fit residues: 128.7099 Evaluate side-chains 283 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 214 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.0040 chunk 212 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18997 Z= 0.232 Angle : 0.561 15.366 25679 Z= 0.278 Chirality : 0.041 0.142 2848 Planarity : 0.004 0.050 3203 Dihedral : 10.736 83.397 2896 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.71 % Allowed : 25.60 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2222 helix: 0.41 (0.16), residues: 1116 sheet: -1.01 (0.34), residues: 221 loop : -1.78 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1016 HIS 0.005 0.001 HIS A 113 PHE 0.022 0.001 PHE F 689 TYR 0.012 0.001 TYR A1334 ARG 0.004 0.000 ARG A 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 209 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.5944 (mp0) REVERT: A 51 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.5190 (ttpp) REVERT: A 53 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: A 54 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6181 (pp20) REVERT: A 62 PHE cc_start: 0.8379 (t80) cc_final: 0.8130 (t80) REVERT: A 74 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8528 (mtm) REVERT: A 90 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6799 (mm-30) REVERT: A 100 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6041 (tp30) REVERT: A 201 LEU cc_start: 0.9097 (tt) cc_final: 0.8853 (tp) REVERT: A 484 TYR cc_start: 0.5189 (OUTLIER) cc_final: 0.4107 (t80) REVERT: A 666 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5156 (mp0) REVERT: A 900 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7129 (ptt90) REVERT: A 984 GLU cc_start: 0.7505 (tt0) cc_final: 0.7178 (tt0) REVERT: A 1063 PHE cc_start: 0.7342 (t80) cc_final: 0.6880 (t80) REVERT: A 1121 GLU cc_start: 0.7648 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 1165 MET cc_start: 0.8488 (tmm) cc_final: 0.8022 (tmm) REVERT: E 10 ARG cc_start: 0.6527 (mtp180) cc_final: 0.6167 (mmm160) REVERT: E 50 HIS cc_start: 0.5942 (m-70) cc_final: 0.5618 (m-70) REVERT: E 120 MET cc_start: 0.7758 (mmt) cc_final: 0.7332 (mmm) REVERT: E 130 ARG cc_start: 0.5786 (ttp-110) cc_final: 0.5436 (mtm110) REVERT: E 191 LEU cc_start: 0.8625 (mt) cc_final: 0.8124 (tp) REVERT: E 216 MET cc_start: 0.6185 (tmm) cc_final: 0.5866 (tmm) REVERT: F 59 ASP cc_start: 0.7562 (t0) cc_final: 0.7247 (t0) REVERT: F 330 LYS cc_start: 0.8537 (tttm) cc_final: 0.8207 (ttmt) REVERT: F 858 ASP cc_start: 0.8415 (p0) cc_final: 0.7933 (p0) REVERT: F 997 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8369 (tp) REVERT: F 1002 CYS cc_start: 0.5271 (OUTLIER) cc_final: 0.3936 (p) REVERT: F 1020 MET cc_start: 0.7923 (ttp) cc_final: 0.7578 (ttp) outliers start: 74 outliers final: 61 residues processed: 270 average time/residue: 0.2762 time to fit residues: 118.7074 Evaluate side-chains 279 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 208 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 542 ASN Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1005 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.0670 chunk 189 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 GLN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105531 restraints weight = 47763.319| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.22 r_work: 0.2956 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18997 Z= 0.143 Angle : 0.520 12.806 25679 Z= 0.258 Chirality : 0.040 0.137 2848 Planarity : 0.004 0.049 3203 Dihedral : 10.406 79.990 2896 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.46 % Allowed : 26.05 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2222 helix: 0.60 (0.16), residues: 1104 sheet: -0.87 (0.34), residues: 220 loop : -1.65 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 187 HIS 0.006 0.001 HIS A 113 PHE 0.025 0.001 PHE F 689 TYR 0.011 0.001 TYR A 108 ARG 0.003 0.000 ARG A 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4197.63 seconds wall clock time: 76 minutes 49.37 seconds (4609.37 seconds total)